I'm afraid that there's very little solid information on how the ninjas in particular utilized anatomy, because most solid information about ninjutsu vanished quite some time ago. The only modern martial artists that have any sort of claim at all to practice ninjutsu as practiced in ancient Japan are the Bujinkan, and their claim is fairly thin from a historical scholar's perspective, though I'll likely take a good deal of flak from Bujinkan artists on YA who say otherwise.
I suggest you change your project's focus to broaden it somewhat, from how anatomy is important to ninjas to how anatomy is important to the martial arts in general. This will provide far more material for your project.
I'll give you a few good topics to look into:
Examine the close relationship between traditional Chinese medicine and various systems of kung fu- they were very often taught side-by-side.
Check out the National Geographic television special Fight Science, remembering that the artist they have labeled practicing 'ninjutsu' is a Bujinkan artist and thus probably not a practitioner of historical ninja arts.
Look into a few of the joint locks practiced by Judo and try explaining them in terms of a joint's natural range of motion.
Explain the relationship of karate's hand-toughening exercises- hitting a wooden board called a makiwara repeatedly- to Wolff's law, the law that bone density increases when the bones are placed under heavy loads. This, among other things, is what allows karateka to break hard objects without injuring their hand.
In your research, make sure you double-check the claims of martial artists and martial arts, even if they are described in explicit anatomical terms- many frauds will try to justify their techniques with medical technobabble, and many people who are qualified as martial artists but unqualified medically will try to explain their techniques in a scientific manner without adequate background knowledge and rigorous experimentation.