A Ninja is someone who is proficient in Ninjutsu
No, just no. Ninjutsu is a martial art, it takes tradition from the classical ninja but it's not the same as being one. In the time of actual ninjas there wasn't even a unified school of martial arts called ninjutsu.
A ninja or shinobi in the sense being used here is an assassin, covert agent or mercenary in feudal Japan. For the ninja it was just as important to train survival and scouting techniques, poisons and explosives, long distance runs, climbing, stealth methods of walking and swimming. The ability to impersonate common professions to take their form in disguise.
For the most part a ninja getting into a fist fight was already a sign he was doing a bad job.
Someone who is proficient in ninjutsu is a practitioner of ninjutsu, that's it. You might call them ninja if you'd like, but there's a reason you don't see all those MMA fighters with a ninjutsu blackbelt calling themselves "ninja", it's ridiculous and they know it. They are ninjutsu blackbelts, as in, praticioners of the current martial art called ninjutsu.
As for Scorpion, you'd notice he was Japanese, lived in feudal Japan when he was a human, and was part of what is called a ninja clan.