Can't see it. It will only let you lock it if 

Automatic Code Setup": true,
"Automatic Code Lock Deploy": true, 

you make those true. Then you cannot unlock or anything.

you cant do /ql It says they arent Quarry/pumpjack

Any fix?

using Newtonsoft.Json.Linq;
using Newtonsoft.Json;
using Oxide.Core.Libraries.Covalence;
using Oxide.Core.Plugins;
using System.Collections.Generic;
using UnityEngine;
using Random = UnityEngine.Random;

namespace Oxide.Plugins
{
    [Info("Quarry Locks", "Orange", "1.3.4")]
    [Description("Add code-lock on Mining Quarry/Pump Jack")]
    public class QuarryLocks : CovalencePlugin
    {
        #region Class Fields

        [PluginReference] private Plugin Clans, Friends;
        private const string PermissionUse = "quarrylocks.use";

        #endregion Class Fields

        #region Initialization

        private void Init()
        {
            permission.RegisterPermission(PermissionUse, this);
            foreach (var command in _configData.Commands)
                AddCovalenceCommand(command, nameof(CmdLockQuarry));

            if (!_configData.AutoCodeLock)
                Unsubscribe(nameof(OnEntityBuilt));
        }

        private void OnServerInitialized()
        {
            UpdateConfig();
        }

        private void UpdateConfig()
        {
            if (_configData.Commands.Length == 0)
            {
                _configData.Commands = new[] { "ql" };
                SaveConfig();
            }
        }

        #endregion Initialization

        #region Configuration

        private ConfigData _configData;

        private class ConfigData
        {
            [JsonProperty(PropertyName = "Enable Permission")]
            public bool UsePermission = true;

            [JsonProperty(PropertyName = "Can Admins Ignore Permission Restriction")]
            public bool AdminsAllowed = true;

            [JsonProperty(PropertyName = "Automatic Code Setup")]
            public bool AutoCode = true;

            [JsonProperty(PropertyName = "Automatic Code Lock Deploy")]
            public bool AutoCodeLock = false;

            [JsonProperty(PropertyName = "Share With Team")]
            public bool UseTeams = false;

            [JsonProperty(PropertyName = "Share With Clan")]
            public bool UseClans = false;

            [JsonProperty(PropertyName = "Share With Friends")]
            public bool UseFriends = false;

            [JsonProperty(PropertyName = "Command")]
            public string[] Commands = new[] { "ql", "quarrylock" };

            [JsonProperty(PropertyName = "Chat Avatar")]
            public ulong SteamIDIcon = 0;
        }

        protected override void LoadConfig()
        {
            base.LoadConfig();
            try
            {
                _configData = Config.ReadObject<ConfigData>();
                if (_configData == null)
                {
                    LoadDefaultConfig();
                }
            }
            catch
            {
                PrintError("The configuration file is corrupted");
                LoadDefaultConfig();
            }
            SaveConfig();
        }

        protected override void LoadDefaultConfig()
        {
            PrintWarning("Creating a new configuration file");
            _configData = new ConfigData();
        }

        protected override void SaveConfig() => Config.WriteObject(_configData);

        #endregion Configuration

        #region Localization

        private string Lang(string key, string id = null, params object[] args) => string.Format(lang.GetMessage(key, this, id), args);

        protected override void LoadDefaultMessages()
        {
            lang.RegisterMessages(new Dictionary<string, string>
            {
                ["Added"] = "Codelock was added!",
                ["Already"] = "That Mining Quarry/Pump Jack already has codelock",
                ["NoLock"] = "You need a codelock to use this command, get one and try again!",
                ["NotAllowed"] = "You do not have permission to use this command",
                ["NotAQuarry"] = "This is not Mining Quarry/Pump Jack",
                ["NotLookingAtQuarry"] = "You are not looking at Mining Quarry/Pump Jack",
                ["Ownership"] = "Only owner of Mining Quarry/Pump Jack can add locks to it!",
                ["Prefix"] = "<color=#00FFFF>[Quarry Locks]</color>: ",
            }, this);
            lang.RegisterMessages(new Dictionary<string, string>
            {
                ["Added"] = "Кодовый замок добавлен!",
                ["Already"] = "На этот Горнорудный карьер/Нефтяную вышку уже установлен кодовый замок",
                ["NoLock"] = "Для использования этой команды вам понадобится кодовый замок, возьмите его и попробуйте еще раз!",
                ["NotAllowed"] = "У вас нет разрешения на использование этой команды",
                ["NotAQuarry"] = "Это не Горнорудный карьер/Нефтяная вышка",
                ["NotLookingAtQuarry"] = "Вы не смотрите на Горнорудный карьер/Нефтяную вышку",
                ["Ownership"] = "Только владелец Горнорудного карьера/Нефтяной вышки может поставить на него замок!",
                ["Prefix"] = "<color=#00FFFF>[Quarry Locks]</color>: ",
            }, this, "ru");
        }

        #endregion Localization

        #region Oxide Hooks

        private object CanLootEntity(BasePlayer player, ResourceExtractorFuelStorage container)
        {
            if (container == null || player == null || container.IsDestroyed)
                return null;

            if (_configData.AdminsAllowed && player.IsAdmin)
                return null;

            BaseResourceExtractor entity = container.GetComponentInParent<BaseResourceExtractor>();
            if (entity == null) return null;
            CodeLock codelock = entity.GetComponentInChildren<CodeLock>();
            if (codelock == null)
                return null;

            return codelock.whitelistPlayers.Contains(player.userID) ? (object)null : true;
        }

        private void OnEntityBuilt(Planner planner, GameObject gameObject)
        {
            if (!_configData.AutoCodeLock)
                return;

            BaseEntity entity = gameObject?.ToBaseEntity();
            if (!entity)
                return;

            BasePlayer deployingPlayer = planner?.GetOwnerPlayer();
            if (!deployingPlayer)
                return;

            if (entity.ShortPrefabName != "miningquarry_static")
                return;

            Vector3 cordinates;
            if (entity.ShortPrefabName == "miningquarry_static")
                cordinates = new Vector3(1.35f, 10.15f, 0.00f);
            else
                cordinates = new Vector3(-3.38f, 6.30f, -0.30f);

            if (deployingPlayer.inventory.FindItemByItemID(1159991980) == null)
            {
                Print(deployingPlayer.IPlayer, Lang("NoLock", deployingPlayer.IPlayer.Id));
                return;
            }

            deployingPlayer.inventory.Take(null, 1159991980, 1);

            var codelock = GameManager.server.CreateEntity(StringPool.Get(3518824735)) as CodeLock;
            var bre = entity.GetComponent<BaseResourceExtractor>();

            codelock.gameObject.Identity();
            codelock.SetParent(bre, BaseEntity.Slot.Lock.ToString().ToLower());
            codelock.Spawn();
            bre.SetSlot(BaseEntity.Slot.Lock, codelock);
            codelock.transform.localPosition += cordinates;
            codelock.TransformChanged();

            if (_configData.AutoCode)
            {
                codelock.code = Random.Range(1000, 9999).ToString();
                codelock.hasCode = true;
                codelock.SetFlag(BaseEntity.Flags.Locked, true);
                codelock.whitelistPlayers.Add(deployingPlayer.userID);

                if (_configData.UseTeams && RelationshipManager.TeamsEnabled())
                {
                    RelationshipManager.PlayerTeam playerTeam = RelationshipManager.ServerInstance.FindPlayersTeam(deployingPlayer.userID);
                    if (playerTeam != null)
                    {
                        foreach (var member in playerTeam.members)
                        {
                            codelock.whitelistPlayers.Add(member);
                        }
                    }
                }

                if (_configData.UseClans && Clans != null && Clans.IsLoaded)
                {
                    string playerClan = Clans.Call<string>("GetClanOf", deployingPlayer);
                    if (!string.IsNullOrWhiteSpace(playerClan))
                    {
                        JObject clan = Clans.Call("GetClan", playerClan) as JObject;
                        JArray members = clan?.GetValue("members") as JArray;
                        if (clan != null && members != null)
                        {
                            foreach (var clanMember in members)
                            {
                                codelock.whitelistPlayers.Add(ulong.Parse(clanMember.ToString()));
                            }
                        }
                    }
                }

                if (_configData.UseFriends && Friends != null && Friends.IsLoaded)
                {
                    var friends = Friends.Call("GetFriends", deployingPlayer.userID) as ulong[];
                    if (friends != null)
                    {
                        foreach (var friend in friends)
                        {
                            codelock.whitelistPlayers.Add(friend);
                        }
                    }
                }
            }

            Print(deployingPlayer.IPlayer, Lang("Added", deployingPlayer.IPlayer.Id));
        }

        #endregion Oxide Hooks

        #region Commands

        private void CmdLockQuarry(IPlayer iplayer)
        {
            BasePlayer player = iplayer?.Object as BasePlayer;

            if (iplayer == null || player == null)
            {
                return;
            }

            if (_configData.UsePermission && !permission.UserHasPermission(iplayer.Id, PermissionUse))
            {
                if (!_configData.AdminsAllowed || !iplayer.IsAdmin)
                {
                    Print(iplayer, Lang("NotAllowed", iplayer.Id));
                    return;
                }
            }

            RaycastHit rhit;
            BaseEntity entity = null;
            if (Physics.Raycast(player.eyes.HeadRay(), out rhit))
            {
                entity = rhit.GetEntity();
            }

            if (entity == null)
            {
                Print(iplayer, Lang("NotLookingAtQuarry", iplayer.Id));
                return;
            }

            Vector3 cordinates;
            switch (entity.ShortPrefabName)
            {
                case "mining.pumpjack":
                    cordinates = new Vector3(-3.38f, 6.30f, -0.30f);
                    break;
                case "miningquarry_static":
                    cordinates = new Vector3(1.35f, 10.15f, 0.00f);
                    break;
                default:
                    Print(iplayer, Lang("NotAQuarry", iplayer.Id));
                    return;
            }

            if (entity.OwnerID != player.userID)
            {
                Print(iplayer, Lang("Ownership", iplayer.Id));
                return;
            }

            if (entity.GetComponentInChildren<CodeLock>() != null)
            {
                Print(iplayer, Lang("Already", iplayer.Id));
                return;
            }

            if (player.inventory.FindItemByItemID(1159991980) == null)
            {
                Print(iplayer, Lang("NoLock", iplayer.Id));
                return;
            }

            player.inventory.Take(null, 1159991980, 1);

            var codelock = GameManager.server.CreateEntity(StringPool.Get(3518824735)) as CodeLock;
            var bre = entity.GetComponent<BaseResourceExtractor>();

            codelock.gameObject.Identity();
            codelock.SetParent(bre, BaseEntity.Slot.Lock.ToString().ToLower());
            codelock.Spawn();
            bre.SetSlot(BaseEntity.Slot.Lock, codelock);
            codelock.transform.localPosition += cordinates;
            codelock.TransformChanged();

            if (_configData.AutoCode)
            {
                codelock.code = Random.Range(1000, 9999).ToString();
                codelock.hasCode = true;
                codelock.SetFlag(BaseEntity.Flags.Locked, true);
                codelock.whitelistPlayers.Add(player.userID);

                if (_configData.UseTeams && RelationshipManager.TeamsEnabled())
                {
                    RelationshipManager.PlayerTeam playerTeam = RelationshipManager.ServerInstance.FindPlayersTeam(player.userID);
                    if (playerTeam != null)
                    {
                        foreach (var member in playerTeam.members)
                        {
                            codelock.whitelistPlayers.Add(member);
                        }
                    }
                }

                if (_configData.UseClans && Clans != null && Clans.IsLoaded)
                {
                    string playerClan = Clans.Call<string>("GetClanOf", player);
                    if (!string.IsNullOrWhiteSpace(playerClan))
                    {
                        JObject clan = Clans.Call("GetClan", playerClan) as JObject;
                        JArray members = clan?.GetValue("members") as JArray;
                        if (clan != null && members != null)
                        {
                            foreach (var clanMember in members)
                            {
                                codelock.whitelistPlayers.Add(ulong.Parse(clanMember.ToString()));
                            }
                        }
                    }
                }

                if (_configData.UseFriends && Friends != null && Friends.IsLoaded)
                {
                    var friends = Friends.Call("GetFriends", player.userID) as ulong[];
                    if (friends != null)
                    {
                        foreach (var friend in friends)
                        {
                            codelock.whitelistPlayers.Add(friend);
                        }
                    }
                }
            }

            Print(iplayer, Lang("Added", iplayer.Id));
        }

        #endregion Commands

        #region Helpers

        private void Print(IPlayer player, string message)
        {
            string text;
            if (string.IsNullOrEmpty(Lang("Prefix", player.Id)))
            {
                text = message;
            }
            else
            {
                text = Lang("Prefix", player.Id) + message;
            }
#if RUST
            (player.Object as BasePlayer).SendConsoleCommand ("chat.add", 2, _configData.SteamIDIcon, text);
            return;
#endif
            player.Message(text);
        }

        #endregion Helpers
    }
}

I changed the "mining_quarry" to "miningquarry_static"

This fixed the cant lock issue and the you can now visibly see the lock now as well.

If you have remover tool as well you will need to change the "mining quarry" to "miningquarry_static" inside the config if you want players to be able to pick it back up