It was bad enough (although, admittedly, convenient) that you could just ~glance~ at a filing cabinet or Metal Box and know that it was empty. But now you just glance at a desk and click one button and BOOM you've looted it. Convenient? Sure, it is. Not arguing that. I just think it's a disservice to the game world.
I can't remember the game (Splinter Cell? Alpha Protocol?), but there was some game where you would go to search a filing cabinet and you'd get a progress bar that ticked down while your character animated flipping through files in a filing cabinet, or shuffling the contents of an opened desk drawer. It was real time so you might have to stop your search before you determined whether or not there was anything in there of note --- a guard walks by, for example, so you stop searching and hide, then the guard leaves and you resume your search.
I just have this mental image of running through a building spamming the "loot all" button while I wave my viewpoint around. Stack of six boxes? No more sliding the cover off one of them and peeking inside and picking what you want and then closing it and opening the next --- now just wave the mouse over them and click click click you've looted them all. Assuming they didn't have the giant omniscient "EMPTY" tag visible on them.
I'm not saying that the old method did not have some exploitative aspects (wait until foe is turned, then open desk drawer and time stops so you can loot it all).... but the new method doesn't seem any less exploitative. Now, you just wait until the NPC is turned away, glance at the desk and hit the loot all button. Unless the actual ACT of looting takes some time, which I don't recall seeing in any videos, then this is simply a streamlined way of looting.
I can appreciate that it makes it ~easier~ to loot everything, faster, but just like putting the EMPTY tag on empty containers, it is more of a meta-gaming thing that (to me) detracts from the game world's believability.
EDIT: Typo.