WYCKID is right; the "ninja" title is just a shortcut name for the many resembling male-masked-different colored characters of Mortal Kombat. "Ninja" is just a quick and easy way to identify them, instead of naming 'Lin Kuei' or 'Reptilian Creature'.
My vote : Scorpion may be "walking-dead" right now, but he was once a ninja. And out of the selection, that gives him the advantage ! Plus he was once chosen as Champion of the Elder Gods in Deception and being basically immortal.. Then again, pretty much all of the Mortal Kombat characters could be immortal-like, since they seem to be resurrected or escape from the Netherrealm on numerous occasions.
When sub-zero says that the Lin Kuei are not ninjas, he is saying so to distance himself from the Shirai Ryu, who didn't have a clan name at the time, so were just referred to as 'Ninjas'.
Sub-Zero's MK1 bio: The actual name or identity of this warrior is unknown. However, based on the markings of his uniform, it is believed he belongs to the Lin Kuei, a legendary clan of chinese ninja.
You all take things too literally.