i think this problem is caused by the engine. this is divinity engine and in divinity series there was a trait "luck'" - higher you have it, higher the chance to find something. so if you don't have luck in divinity you will find a bunch of empty crates but if you do, you can find a lot of appearing stuff in these same crates.
bg has fixated loot so this doesn't work. i guess they decided to fill the crates with something, and that is how we ended up with so many rotten carrots and sandals.
personally i would preferred less crates with better stuff in them. maybe one day we will get closer to that dream...