I don't want to see empty containers removed. Instead what I would like to see is a direct visual appearance for when a container is empty or not.
Bookcases would have empty shelves if they are empty. Bookcases that have items would show some items they contain such as books or scrolls.
Potion racks will appear empty if they are empty, but will contain bottles if they are not.
Barrels, chests, and crates would appear open if they are empty, but will be shut if they are not.
Armor and Weapon racks will appear empty if they are empty, but will contain relevant armor or weapons if they are not.
The list can go on.
Preferably, I would also want it so that you could not put anything but appropriate items inside a container; i.e. no putting weapons in potion racks, etc. Barrels, chests, and crates being the exception, having no limitation on what can be placed inside.
Obviously, this would take alot more effort than simply mousing over a chest and having it say (looted), but I think it would be worth it.