Scorpion, Sub-Zero, Noob, Smoke, Reptile, Cyrax, Sektor, Takeda, Kitana, Jade, and Mileena all at least act the "role" of a ninja as professional assassins, spies, or thieves. There may be techincal differences due to cultural differences like not being Japanese, lol, but other than that they serve the same function. Ermac and Rain do not so they break that mold and are "ninja" in visual design origins only. Haven't seen enough of Scarlet to judge and Tanya is only included in the group because she was originally a replacement for Kitana in MK4 (which shouldn't count because that fact alone would make Sindel a ninja, lol, because she was "not-Kitana" in MK3).
Erron Black is more in line with Kano, Kabal (also wears a mask is he now a ninja??), and other Black/Red Dragons. I was actually surprised in MKX that he DIDN'T turn out to secretly have been working with Kano and was a Black Dragon the WHOLE time.
Edit: yeah I forgot Tremor, lol. Add him to the Scarlet list as I'm not sure whether he's more ninja, merc, or other, lol.