I was at a martial arts center that taught Ninjutsu along with some other martial arts and what one of the instructors said about the classical all black Ninja uniform is that it originated from Japanese stage workers. When they would put on performances on Japanese stages they would have people who would help with some of the stuff that had to be done on stage but that the audience was not supposed to see them and that's why they wore the all black uniforms and that its basically the same way with the Ninja, people aren't supposed to see them. Basically Ninja are supposed to blend in and be unnoticed and while the classical all black uniform might not always be the best way to do that, that's where it originated from, from stage workers. At least that's what the instructor claimed that that's where the uniforms came from.