I'll torture the devs with a suggestion that's feasible, yet probably annoying to implement:
The ability to visit a location in a period prior to it for the purposes of scouting and stashing certain items in places you know about, effectively replacing the stashing system by requiring you to move the item there before you use it. (Those areas could be marked as concealed areas, or perhaps replace body bins/storage.)
I'm sure that in terms of geometry that's not too bad, but in terms of engine stuff it's probably a bridge too far. It's the one thing I kept thinking about: pre-scouting. Of course it should have consequences if it's too suspicious or something, but this, again, is probably in the realm of too annoying/difficult, unless there's a guard or something that flicks on when the drop-spot is active.
Failing that, perhaps just a guard or extra person who looks at an area when the agency stashes things there. A suspicious civilian, or an armed person, doesn't matter (could vary?), adding a bit of risk to using certain drop/pickup spots.