Movable and interactable containers such as barrels and crates have become a staple part of Larian's games.
I doubt anyone actually enjoys playing a Dungeon Janitor that systematically sweeps through every container just in case one of them happens to contain a healing potion or spell scroll, but I can still appreciate the containers' presence for the sake of serving as decoration, stage set pieces and movable scenery.

I think the easiest way for them to remain in the game without causing people to feel like they're wasting their time scooping through them all would be to add the (empty) suffix that becomes present once you've already opened the container once. It'd allow us to keep them in the areas without slowing down the game every time you enter a new cellar full crates.