What ninja is any good at their job if they do not have high mental discipline and the ability to easily control how their own mind? Self-Hypnosis is only a more active form of Meditation after all. And something Ninjas, and really all High Level Martial Artists are known for, is meditating.
Meditation is Understanding your mind. Why you think and feel the way you do, how thoughts flow thruogh your head, and so on. This understanding allows one greater control, leading to increased focus, better memory, and if one is to believe in Ki and stuff manipulating the very essence of you to perform Magic.
Hypnosis, self and otherwise, is the Manipulating of the mind. Understanding the specific mind in question is helpful, but not necessarily needed. It is the direct approach to what Meditation offers indirectly. We purposefully control our own mind, allows us to do things like fall asleep at will rather than laying and waiting for it to happen, attain great focus by keeping our brain away from distraction, Ignore Pain, push our muscles past their natural limits, slow down our perception of time, carry out acted roles with perfection for, for a short time, we ourselves believed we were who we said we were, and more.
Meditation and Self Hypnosis also lets us develop our skills so that we can become ready for prime time faster. But Shadow-Boxing is only good for martial skills, while Meditation and Self Hypnosis is good for all skills.