Is there a way to disable the carlift codelock option, when a car is on the lift, that has a codelock applied by VehicleDeployedLocks? If not, would it be possible to implement it?

Not currently. I was thinking of trying to integrate the vanilla feature somehow with this plugin, but it may be tricky and nobody had asked for it yet so I completely forgot about it.

Simplest would be to just disable the built in car locks. Here's the code for a simple plugin that can do that. Save it as NoCarLocks.cs.

namespace Oxide.Plugins
{
    [Info("No Car Locks", "WhiteThunder", "0.1.0")]
    [Description("Prevents players from adding vanilla code locks to cars")]
    public class NoCarLocks : CovalencePlugin
    {
        private readonly object False = false;

        private object OnVehicleLockableCheck(ModularCarCodeLock carLock)
        {
            // Return non-null to prevent the car from being locked.
            // This has the effect of not even showing the lock option to players.
            return False;
        }
    }
}