I found 2-3 bones/remains in a pit that had no label
I must've missed those. Where'd you find 'em? Could be intentional, could be simply a forgotten label. I dunno.
I can't remember the exact location off the top of my head (in some caves, I think the only NPCs on the map are Cave Hoppers), it has a really notable pit filled with bones but I don't think there's anything hostile there.
I also know there's a hidden footlocker like that south of Rail Crossing, on the west side of the railroad tracks leading south.
Oh, I remember that one!

I love hidden stuff like that!
Aaand there are also some other unlabeled objects, like the secret passage leading to Kohlmeier's old house in Junkyard. I think that's actually a very good idea. Players can find it without "unlocking" it via a quest flag or perception points or something, and Kohlmeier's description of it really helps simply because you know where to look. More secrets like that would be nice.
I agree, there are some potential benefits to leaving some things unmarked (though if this is going to be the case some things should probably just not be marked otherwise players will assume everything is marked).