I doubt that real ninjas got into hand-to-hand fights if they could help it. Kinda goes against the idea of an assassin striking from stealth. The whole "ninja fighting" thing is probably an invention of the stage and films.
The idea of ninjas wearing black, by the way, is definitely from the stage. Real ninjas would've dressed like normal people to blend into a crowd. But in Japanese theater, the stagehands wore all-concealing black and were treated as invisible and nonexistent by the players and the audience. So when they wanted to portray a ninja making a surprise stealth attack out of nowhere, they'd have the "ninja" player dressed in black so as to blend in with the stagehands and be ignored by the audience until they shockingly struck down one of the other players. Thus the myth of ninja invisibility was born as well as the myth of ninja fashion.
The idea of ninjas wearing black, by the way, is definitely from the stage. Real ninjas would've dressed like normal people to blend into a crowd. But in Japanese theater, the stagehands wore all-concealing black and were treated as invisible and nonexistent by the players and the audience. So when they wanted to portray a ninja making a surprise stealth attack out of nowhere, they'd have the "ninja" player dressed in black so as to blend in with the stagehands and be ignored by the audience until they shockingly struck down one of the other players. Thus the myth of ninja invisibility was born as well as the myth of ninja fashion.