Because Shao Khan doesn't give a fuck about what they really want to call themselves, he's an ass like that. :/
Bi Han (Older Sub-zero and Noob Saibot) has stated many times before how much he hates being grouped in with "Ninjas" like Scorpion. This would go with the rest of the Lin Kuei as well (Smoke, Cyrax, Sektor, Kuai Liang). They are all specialized assassins. They are hired, similarly to Scorpion's ninja clan, to do certain missions, but aren't actually ninjas. More on that in a sec, I want to go over the other characters really quick.
Reptile and Ermac are not assassins, they are high ranked soldiers for Shao Khan's army. Pretty much extremely strong henchmen. His stealth doesn't instantly make him a ninja. Noob Saibot is nothing more than a slave to Quan Chi, in his past life he was Lin Kuei. Now he is a wraith. Rain is... well more difficult.
Rain betrays anyone he can for who ever is stronger at the moment, he really doesn't have a faction outside of his own. He is definitely not an assassin, though. His exact definition is hard to describe, but he isn't a ninja.
The females are a bit more interesting though. Mileena was created for the sole purpose of killing (pretty much) but she also isn't a paid assassin. Same with Skarlet, they are both just very high ranking soldiers for Shao Khan. However, they both come closest in terms of an ninja for the females, yet aren't really there.
Kitana and Jade are pretty much enforcers. All the other high ranking soldiers? They rank higher. Assassins, yes, but not paid assassins, which is important in the definition of a ninja.
Next, that link you gave states that the term is loosely used in the Mortal Kombat universe to group all the ninja garb wearing characters, who dress somewhat similar together because that is a mouthful.
Finally, I want to mention the fact that by all means and definition, the Lin Kuei (early in the history) are pretty similar to a ninja clan. Paid assassins trained to carry out special missions and so on. The biggest difference between them? Heritage. Ninjas are Japanese. They were originally a group created to stop the oppressive Samurai centuries ago. The Lin Kuei has basis in China and Chinese culture, but are worldwide. They're like the Planeteers had sex with the Power Rangers or something (hawt).
Just as it's disrespectful to say a Japanese man is just the same as a Chinese man, it's wrong and disrespectful (yes, to a fictional faction, I know) to compare the Lin Kuei to simple shinobi.
tl;dr
Mileena and Skarlet are the closest things to female ninjas, most other ninjas are soldiers and not actual shinobi, heritage and culture separates the Lin Kuei from being just a ninja faction.
Do I look too far into this stuff? Yes. But it killed some time, so yay.
