I went to TWRP, selected "advanced wipe" and checked every box, including "internal storage". It turned out it deleted the OS too, but I had Nexus Toolkit on my PC, so I flashed stock 4.4.3 image (it warned me it will fully wipe the device, which I actually needed). Booted it up and everything worked fine.
But just to be sure, because all of this was last-minute, I want to ask two questions:
1) Did I really wipe all my internal memory, including pictures, downloads, and stuff?
2) Will the device be working fine?