Yea but it's common knowledge that both Samurais and Ninjas did exist. We aren't stupid, what Hikyuu ment was when was the last time i saw a ninja. He never said that they didn't exist.
As for that about the natural powers and shit i will call that bullshit until i get some proof(A real life ninja, if there are any in this day and age that displays some jutsus where natural powers are involved.). For now it's like all other bullshit things like Ghosts, Aliens, Vampires and such. Until i get some proof i don't believe it.