Recruited from Ninja Houses.
Ninjas were formed from bandit clans sometime in the 10th century. These bandits mastered the arts of combat and warfare in the form of what we call ninjutsu, ninja art. Though there common use as assassins is infrequent in history there use as mercenaries is what they were commonly used for. This is the reason why they also appear as units.
The Ninja is trained from birth for spying and assassination. Enemy Daimyo, Generals and Emissaries are all possible targets. The more senior the target the smaller the chance of success. Ninja get more effective each time they make a kill.