Ninjas Were Probably More Like Spies than Assassins
Even if they only exist as mutant turtles, everyone is familiar with ninjas. Ancient Japanese warriors in disguise, armed with lethal weapons and unhuman stealth. They have long been a mainstay of popular culture. It turns out that they were also largely born there.
It's not as though ninjas didn't exist. However, ninjas as we know them did probably not. There is reason to believe that most of what we think we know about ninjas is based on myths, theories, exaggerations, and supposition because the history of ninjas is, at best, vague.
According to what is known about them, they sound less like cunning assassins and more like vintage CIA-style intelligence agents who, of course, occasionally commit murder.