I think we should be given an automatic keyring container that holds all the keys, no mess and has the chance of use if we need a key again for whatever reason.
Just add a key ring.
This was already in "Realms of Arcadia" from 1991.
You could buy a key ring for a few coins in every shop.
When you find a key, you could drag it to the ring and it was added (the key disappeared in the inventory)
Double click on the key ring and you could see a list of rings you have.
You could sinmply use the key then (it remained on the ring and was not added back to inventory when used).
I was thinking of what Resident Evil did, notifying the player the key would be out of uses. But a keyring is nice and can keep the inventory organized.