Good and bad is a little subjective and situational, what is good for one game might be bad for another, but I do agree a game should be made as a complete package first before considering mods.
On topic I think keys disappearing could create new issues where only one person goes through the door and the rest of the party gets stuck, or you need that key for multiple doors/containers and by using it once you lock out the other things. Or worse, you somehow relock a door and now that the key is gone you are stuck. Therefor I think its better for them to go into a keyring item so it does "disappear" from your inventory not clogging things up, but is still usable just in case. It would solve the problem without possibly creating new ones.
True... if there would be an option to lock previously unlocked doors or chests again, of which there isn't. Keys are considered simple one-use-items. You unlock something with it once and it stays that way. Hence the used key has lost it's worth. And about the argument that one key might be needed for multiple things, don't worry, that is really no issue to program to make it work without issues.
