Hellfire is the best variation because it makes the best use of all Scorpion universal buffs, besides you can fbc your mixups, flame aura and hellfire makes a lot of difference in MUs where you can't use ninjutsu's swords, and the FBC pressure is still there if you can condition your opponent to not back dash, or armor through it.
Ninjutsu is good and effective, but there are still MU's which is plain horrible using ninjutsu, as much as his both F2 and B2 cover some good ranges, they're are not safe by any means and should be used sparingly, B2 is -17 and F2 is -11, B4 is -4 on block but is 13 frames, in this game 13 frames is slow due the pace of the game being a lot faster, even 11 frames is somewhat slow if the move doesn't hit mid and cover a lot of distance.
Ninjutsu requires much more fundamentals to play effectively, since his only tool that crushes low sometimes is F3, but he has to spend a bar to hitconfirm and stay safe at the same time, Hellfire doesn't even need F3, but then again, you can FBC F3, and hitconfirm if you crush a low, or apply pressure if blocked.