Here's an incredible post by /u/AsiaExpert on this topic.

Ninja were clandestine operatives, often used for intelligence gathering and special warfare. The trope of the black clad, masked man sneaking into castles isn't horribly unprecedented, but their feats have been exaggerated. Moreover, the trope presents a very incomplete picture. According to Stephen Turnbull of UC Berkeley in California, ninja present a significant problem for historians for if a ninja succeeded their operation, it would likely have gone unknown. Examples of their activity include observing enemy movements while disguised as peasents. More dramatic activity includes the use of simple explosives and grappling hooks to break into fortified zones. Rumors surround the death of warlord Uesugi Kenshin. He began hemorrhaging in the middle of the night, and quickly died. His death was so timely for his rivals, that the possibility of hired ninjas is still entertained.