Well, as long as there's nothing hostile aware of you, you're pretty safe mucking out your inventory. Going into and out of it are free, but actually equipping, dropping, or using an item cost. Next game I'll probably make it free; it wound up being a case of realism getting in the way of fun.
I've debated having a notification when a level is clear, but just never got around to it. I might still do it at some point, but QuickHack's low priority at the moment; I consider it done, and just come back and tinker every now an then.
I haven't gotten a lot of feedback on the tokens; my feedback overall has actually been pretty limited. I personally clear the room (but not the level) before picking them up. My wife is terrified by them, but can't resist the possibility of sweet, sweet loot, so she will clear earlier levels before picking them up, or just the room in later levels. She only skips them if she's out of potions and wounded.
As there's no hunger mechanic, if I get a detrimental effect, I'll often just wait until a monster wanders into the same room as me, or the effect expires.
Also, it's subtle, but you know that little yellow exclamation mark when an enemy becomes aware of you? That means they're surprised for a turn (1.0 seconds, regardless of their speed). If a critter does wander in while you're organizing your backpack, you'll have a little time to react.