MK lore is incredibly messed up. You have Japanese ninjas, Chinese ninjas, Hellspawn ninjas, Cyborg Ninjas, and Good ninjas! And then you have Kung Fu badasses, warrior princesses, alien clone princesses, SWAT team guys, SWAT Team Girls, Necromancers, Immortal chinese dudes, literal gods, inter-dimensional conquerers etc etc.
You also have a character called ‘Smoke’ in MK (SMOKER)
But, as @GRAG said, actual Ninjas dressed like farmers/merchants/streetfolk to blend in.
Inverse Power Ninja is more like Mortal Kombat ninjas due to a) face mask, b) kunai on chain thing (Which Scorpian uses to make the other people GET OVER HERE), and c) rad looking leather armour that reveals a lot of thigh.
Glorious Ninja is kind of like Hayabusa from DOA/Ninja Gaiden, but again, doesn’t really look like a farmer.