Hmmm, I dont think a perception check to give you a INDICATION of the whereabouts of valuable loot would be bad no. But I wouldn't make crates inaccessible per se. ANd I would make these things optional. I personally don't check every crate lol. Especially if 3 in a cluster have already been empty. But auto pick-up loot? ehmmm... is clicking to pick up an item really that tiring? xD.

I get people would only want to spend as little time looting as possible these days. Same thing with endless backtracking. Hence why nigh on any rpg with a semi open-ish world has fast-travel these days. Not sure where the sweet spot would be in this really. Clutter is needed to make a world feel lived in to some degree. Being able to pick up a good portion of it, makes it feel a little less static, at least to me. I've been long since cured of taking everything nailed down with me xD. Fallout and Skyrim punished you well enough for that (ah the long slow walks beacuse you couldnt fast travel :D). I mean why would I take non magic loot with me? Maybe in the early stages it can make you some money, but asuming that at full release you also get some money for questing, I hope this is not that much of a necessity.

I assume things will be streamlined clutter and lootwise, I personally do not really wish to turn this into a: press F to loot entire dungeon game.

But maybe some narrative driven at a glance looting like Merry Mayhem described could be a alternative. I quite liked the narration based secrets you could find in Pillars of Eternity 1 and 2 well enough. Maybe this would also be a option for some hidden shortcuts into areas, utilising more of the athletics skills and such. or finding a use for items such as... rope? laugh.

I dont really remember how much the loot availability changed during EA of DoS 2 and full release, but I am sure they will figure out a middle ground to satisfy both the kleptomaniacs as the more casual looters among us.