Ninjas were real. But they weren't like their pop culture depictions.

So in Japanese stage plays, it was common for stage hands and prop handlers to wear black clothing. This was kind of their costume, and a sign to the audience that they weren't part of the play itself. Basically, if an object or puppet or something was being moved by someone in black, you'd interpet it as the object moving on its own instead of being moved by someone. This idea was borrowed for art, where ninjas would be "hidden" by being dressed in black. Some stage plays would even make use of this where one of those stage hands would turn out to be a ninja hidden in plain sight.

But in a way, that did sort of reflect reality. Just as the "ninjas" in a play were hidden by being dressed up as part of the crew, real ninjas - who should be more thought of as kind of special forces, not just conducting assassinations, but also reconnaissance/spying, etc - would often dress as common every day workers. So they might hang out at a castle disguised and behaving as a gardener, or mason, or what have you. Blending in with the people, they could collect information about the comings and goings of people, the routines of a castle, or maybe help move precious cargo by being security without drawing attention, or perhaps pretending to be pilgrims on the road in order to set up an ambush, things of that nature.

Pure black itself isn't that useful even as camouflage, since rarely are things a straight black color. Even against the night sky, a black clad person will be silhouetted against sky because even the night sky isn't perfectly black. Night time operations probably saw the use of darkened clothing, perhaps using coal to blacken shiny tools, etc, but by no means is there any evidence for any kind of black ninja uniform, or for any kind of standard uniform for that matter. More than anything, they'd lean towards practicality, and black is rarely that practical outside of maybe a cocktail party.