Soft buttons disappeared At one point screen just become bit higher. Buttons gone, and it's not that funny, as it can seem. Phone become literally single-task and I had to reboot just to switch application. Found some software emulator that helps me to survive at the moment, but question is how to get buttons back? No, reboot obviously didn't help, I also flashed new version of CM just in case (was CM 10.1.3 stable, upgraded to 10.2 M1). Same shit. 

Thought about may be I'm darn stupid, and somewhere there is just single option in setting. Either there is no it, or it's name really differs from what I expected (or I'm really darn stupid).

Any clues, guys? Next obvious step is factory reset, but I'm not mentally ready yet.

P.S. Phone is Nexus 4, firmware mentioned earlier.
There is a mode in CyanogenMod and other ROMs called "Expanded Desktop". If your phone is in Expanded Desktop mode, then the navbar will not be visible (The notification bar may also be hidden, depending on your settings).

The easiest way to check if you're in Expanded Desktop is to try toggling it. Simply long-press the power button to get CyanogenMod's expanded power menu, then tap "Expanded Desktop" to toggle it.

If your buttons showed up after doing this, then you're set! If not, it's something else.