I mean, if we want to talk about realism, the fact that so many crates and barrels even exist in a relatively unpopulated area with no sign that there was ever a cooper to make them or anyone manufacturing enough goods to need that kind of storage. That's a lot of materials and labor spent on something that isn't really needed (especially as evidenced by the fact that most of them are empty). It might make sense for the Zhents to have a bunch of crates, but that's about it.
That said, this is a game, not a simulator. We don't need everything to be completely accurate - just reasonably believable. It might be that these "empty" crates are actually full of stuff that we don't need and so the game just doesn't tell us about them. I'm not going to lug around a crate full of coffee grounds or bolts of cloth or anything like that - "empty" just means "empty of things that are useful to me". This is fine, except:
1) It would be more believable if they represented that the containers were full of stuff we didn't need. Having a character make comments like "This whole crate of almonds has gone rancid." instead of saying "empty" would make the world feel a little more lived in.
2) It would be more believable if the world weren't already full of so much junk that we don't need. Abstracting away the contents of crates, but letting us pick up every cutting board and bone and spoon is pretty ridiculous.
3) Who is leaving individual gold pieces in these crates? I can think of reasons why an individual might do that, but it's so widespread as to be ridiculous. Why did none of these people (or whoever killed them) take their gold with them when they left?
Let's separate the problem from the solution(s) here. As I see it, the issue here is that searching through the myriad containers is tedious and breaks verisimilitude and the payoff is disproportionately small. Does that sound about right?
Designing a solution (which we aren't empowered to do, but we all know that we like to try anyway) doesn't really work until we can agree on the problem. This one gets tricky, because it ties into the inventory system, the item/gold economy, and (assuming the implement one) the crafting system.
Personally, I'm all for getting rid of individual containers and adding a "Loot Area" button tied to a group investigation check. Even in games where looting is simple and easy, it feels boring to me, so my preference is to speed it along as much as possible. I know not everyone will agree with me - that's fine. It's more important to agree on the problem than the solution at this point.