Kind of a loose interpretation of "hotel" - but on Mt. Fuji the huts charge to use toilets unless you're a guest. Not unreasonable, though, given the amount of people coming through and the lack of plumbing. And the last time I was there, most of the huts still worked on the honor system, with a little box at the toilet entrance to leave payment.
Not that I don't believe you, but don't take that to be a common occurrence in Japan at all. By and large, Japan is a safe haven of clean and comfortable public restrooms. There are always exceptions, of course.
Oh, I don't think it is--haven't lived there but have spent some time for conferences and surrounding time. However, just pointing out, it's not unheard of.