I’m in a mil base full of zombies with a sniper rifle, I’m in a guard tower, and I can’t see a thing from up here - is there something I’m missing in the controls, or… ?
Well, in general I can say: Yes. I explicedly mention “in general” since it wasn’t always possible and in the odd case you’re still playing 0.C stable or something, it would be a “no”.
Since you didn’t state a specific version, I guess you’re probably playing on 0.F(rank) or newer.
If that’s the case, you can aim and shoot at another z-level if you set the Options → Debug → Experimental 3D field of vision to true.
After changing that option, you might have to restart the game (or at least reload the save) for it to take effect.
Then you can aim with the weapon and then use the up/down keys (default: “<” and “>”) to view another z-level, up to the maximum you’ve specified in the option Vertical range of 3D field of vision (or the maximum range of the weapon).
To my knowledge it’s still a bit buggy (unless it got changed/fixed), so I highly suggest to stand right on the edge when firing downwards (even then it might still hit the tile you’re standing on).
Appreciated 
Anything is better than being explicitly blind to what’s above or below.
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My few attempts with trying to attack from high ground have all failed miserably. Standing on the very edge of a roof, rocks launched by a staff sling just disappear (not on the roof, not on the ground, and no hit on the monster). Standing at the top of stairs and attacking the monsters that block the ability to descend have resulted in all the rocks hitting the top of the stair.
Supposedly it’s possible to hit monsters in the stair scenario using reach weapons, but I haven’t been in a position to try that.
I have been able to attack upwards to hit flying monsters on a few occasions.
Note that the 3D view is experimental and not enabled by default for a reason. I haven’t seen anything indicating it’s worked on for quite some time, though.
You may find that whatever is above you being explicitly blind to you might be preferable to mutual visibility…
you can see below z levels by enabling experimental 3D mode in options, but i’ve noticed that 90% of the time you’re shooting up or down you’ll miss completely. And whatever you do don’t try and use the flamethrower since the wonky targeting will end up setting yourself on fire if you’re not extremely careful and fire very far away