It is a bit frustrating. That said, a convenient way of dealing with them in Larian games since (at least) Divinity 2 has been to do a whirlwind attack to "open" a bunch of them at once and collect any resulting loot.
This just made my day.
How about implementing a mechanic inspired by tabletop D&D - you enter a room and make an investigation/perception roll akin to telling your DM you're looking for anything interesting or out of the ordinary. If you roll well, containers with potentially valuable items light up. This way most characters would be able to find the best pickings fast and if they want to be thorough they can search each container manually.
This wouldn't really work if all you're looking for is an apple though.
