If you hang out at forums like Martial Talk, you will discover that there is a fair amount of discussion regarding the history of Ninjutsu. Generally speaking, there is no real record of ninja before about 1956, and Takamatsu more or less defined the genre. The common belief is that he just created it, and Hatsumi, with his marketing brilliance, has expanded it. The 900 year history is an urban legend.
I say this: So what?
What I, you, my training partners and the Marines are looking for is a fighting system that works. If Takamatsu invented one and it works, who cares? Ueshiba invented Aikido and it works for what it is designed for. Kano invented Judo and it works very nicely too.
I think the problem lies in the same as the one of religion. If something that God or Jesus said is proved to be irrevocably false (like absolute proof that Mary wasn't a virgin, for instance) then large pillars of Christianity fall. If the premise that Hatsumi isn't teaching the art of 33 people before him falls, then again, the Bujinkan will lose a fair amount of identity.
And no one likes to see that.
Don't worry about identity. the implication of that is that you have to be willing to waste a little time studying with someone that turns out to be not what you want then leave. But if that means you find the teacher that you do want, then it was well worth the effort.
That's what it all comes down to - learning what you want to learn. The only kicker is this - be realistic. If you are studying ninjutsu and learning to break bones, don't think you can take your skills to MMA - they don't like broken bones there. If you are studying Aikido and think you are going to go fight on the streets of New York you might want ot reconsider. The art depends heavily on a trained uke.
So - conclusion. 1) Don't worry about history, worry about now. 2) Find an art that works for you, taught by a teacher that works for you. 3) be realistic. Words to train by. Have a nice night.