heya
as mentioned, the lootable option is fixed in the next update. this option will not fix your issue, it can only prevent it. like turning off the water to a leaking pipe, the leak (bug) still needs repaired or the pipe replaced.
I see nothing in the Kits plugin that could cause this to happen.
my understanding from your initial report is that a person's inventory can contain 2 items in the same exact inventory slot. seeing two different weapon models is normal, having two different items equipped in the same slot is not. that requires something to bypass the game's native inventory/wear validation, such as another plugin overriding CanMoveItem or CanWearItem. neither of which is used by the Kits plugin. the Kits plugin contains CanWearItem, but not as a hook, only as an internal helper method.
send me the configs, data files and plugin .cs files for all 3 plugins in a private message. Kits, RaidableBases and CopyPaste. if I am unable to reproduce with your exact files, then the issue is still caused by another plugin (or harmony mod). either way, I don't mind helping you locate this issue. it's interesting enough =p