To fix this issue the CheckHelper needs to be changed to this

		private bool CheckHelper(BasePlayer player, BaseEntity entity)
		{
			if(entity == null || player == null) return true;
			if(player.IsAdmin && AdminCanLoot) return true;
			if(permission.UserHasPermission(player.userID.ToString(), AdmPerm)) return true;
			if(UseZoneManager && ZoneManager != null)
				if((string[])ZoneManager.Call("GetPlayerZoneIDs", player) != null)
					if(IncludeZoneMode)
						foreach(var zoneID in ZoneID)
							if((bool)ZoneManager.Call("isPlayerInZone", zoneID, player)) return true;
			if(entity is SupplyDrop) return true;
			return false;
		}

This will allow it to work correctly with ZoneManager if set to use and exclude plugin checks.

  "UseZoneManager": true,
  "ZoneManagerIncludeMode": false,​

  "UseZoneManager": true,
  "ZoneManagerIncludeMode": true,​

the plugin work only in zones.
So, for PVE server with PVP zones use "ZoneManagerIncludeMode": false and for PVP server with PVE zones use "ZoneManagerIncludeMode": true

You could do that but its not needed with what I posted. I Have both PVP and PVE servers, several of them (30+) - If there is  a Zone and you add it to the config, the 2 checks is all it needs. 

The code posted is cleaner as well as what you have would work, but it again can be more simplified is what I am saying. 

Just letting you know.