Real ninjas had nothing to do with the heroes in black suits from movies. These people were spies and assassins in medieval Japan. Most likely, they were really good at martial arts but they definitely didn’t wear dark clothes and masks. A ninja’s goal was to blend in so that they could watch for the person of interest.
And this line of work was not respectful: their methods were considered dishonest, unlike the work of samurais. By the 17th century, there were almost no ninjas left. But the stories about them were still there: ninjas were believed to have supernatural powers like the ability to walk on water or move without making a sound, for example. But these are just stories and nothing more.