Well, while you edit a room, at least it doesn't show the items which are already being used in another room. So that's something

If you'd want to see which room items are used on which knuffel's room, I'm afraid all items used or not, would have to be visible in the editing room page. But that's pretty messy if you ask me. The used items would have to have some red border or something. So I think it's better that the used room items don't show at all.
Unfortunately you'd have to visit every knuffel's room and click the Empty button to empty all the rooms. So manually, I'm afraid.
I can see how this may be a little troublesome with tons of knuffs. But I think it works pretty well the way it does.
Technically you could suggest the feature: Empty all rooms button in the main Rooms page (entered directly from the Knuffel tab in the menu). Maybe each knuffel from the list could have a box to be marked. So you could mark the knuffel rooms you want emptied.