Here's the thing. If it were the case that getting gems involved the possibility of needing to defeat bosses on the way, I would say there's no way that monsters should spawn gems, because you'd be skipping a part of the experience. But because, upon encountering a boss blocking the way to a resource, you can just go to another chunk where that won't be the case, it doesn't really make a difference. Similar thing with stashes. If the traps around all stashes were implemented, I'd say there's no way a regular monster should spawn the stuff you can find there. But because this doesn't exist, and perhaps even if it did exist you could just do the same thing you can do with bosses in caves, it doesn't really matter. This is where the game suffers from 'too much stuff'. If each tile had 1-2 chunks, most buildings were tiny with a few exceptions, and you only had 1-2 caverns initially, and maybe 3 stashes, you'd treat everything differently. The importance of these strategic resources would skyrocket, and the game would suddenly be very tense as you strive to make best use of what you have. You'd immediately need to start thinking about pushing back the storm. But that's not the case, so everything has low importance, and this turns gem and stash runs into 'grind', and this is unfortunate.
Truthfully though, I'm ok with the game being incentive-neutral with regard to fighting monsters. Good combat mechanics make for better incentive than reward for me, and I enjoy fighting the monsters (though oddly enough, with the keyboard -- not with the mouse).