Read a book. Yes, it is that simple. Ninjas were ssssssoooooo secret they wrote themselves out of existence? Please. If they were so prolific, here would be a historical reference somewhere before a fictional story was ever written.
I definitely understand what you're trying to say, blindly believing anything you read is naive, and if you have any info to disprove his work then i would honestly love to hear it. I do believe that a lot of what he says is credible, but as you've said I have no proof of it, i myself hate being fooled and if you can disprove anything he puts forth then please do share.
as for the ninja thing, feudal japan was a very hard place to live if you weren't a samurai. I doubt that the ninja would have survived very long if anyone actually KNEW anything about them. of course this is based off my observations from reading what he puts forth in his books, so again if you can disprove anything he says about ninja history then please do, i find his
version of it fairly believable though.