Okay, I just asked my Japanese friend. I asked how how she would read it, and she said that she can related it to the "boss" if it was read as shinobi kashira. "Nintou is like, it's sound with no meaning to me. Maybe in a certain sentence, but in the case you're thinking of, 'head ninja' would be shinobi kashira."
She's 25 and a native Japanese speaker, so I trust her with all my Japanese dilemmas. I'll take her word for it. So guess I was wrong in my first post.
In either case, I'd just type it out as にんとう anyway, since it's faster. If you have any other questions you want me to ask her, let me know.
She's 25 and a native Japanese speaker, so I trust her with all my Japanese dilemmas. I'll take her word for it. So guess I was wrong in my first post.

In either case, I'd just type it out as にんとう anyway, since it's faster. If you have any other questions you want me to ask her, let me know.

