NO.
Scorpion was not missing because NRS didn't want him in.
That's a false assumption that many people are under.
"Well, Scorpion wasn't in MK3 because NRS didn't want him in."
NO. FALSE.
The reason that Scorpion wasn't in MK3 was because Daniel Pesina (who played all the ninja characters in previous MK games), was fired for promoting another game (Bloodstorm) in a Johnny Cage costume along with his brother Carlos Pesina.
Bloodstorm was a rival with Mortal Kombat.
It's the same reason why there's no Reptile, or masked Sub-Zero in MK3 either.
The only "ninja" in MK3 was John Turk, who was maskless Sub-Zero
Carlos Pesina was forgiven and now works at NetherRealm Studios again.
During the fallout of Daniel and Carlos Pesina, Carlos' character Raiden was also suspended from appearing in Mortal Kombat 3 and Ultimate Mortal Kombat 3, because they didn't want to use his likeness, as a form of punishment to Carlos.
It wasn't until Ultimate MK3 that John Turk finally donned the Ultimate MK3 "ninja" costumes which brought Scorpion, masked Sub-Zero, Reptile, human Smoke, Noob Saibot, Ermac and Rain into Ultimate MK3.