The success percentage of the Ninjas is extremely low, but any higher could make the game really easy. And a ninja can take a well protected Daimyo without the good luck is not realistic.

So dont take the Ninja attacks as your primary battle plan. Train Ninjas constantly, and send them to enemy one by one, until one of them take the enemy Daimyo suprizingly.

Remember: the game engine just dont want you to able to train a "Super Ninja" who can take out any Daimyo. It is what Geisha's for.