According to Wikipedia, Black Manta is autistic... I have seen nothing to indicate this. It also says that Legion is autistic, which I think is an insult to autistic people, given that Legion is insane and has multiple personalities.
Also, while Nobu might be more skilled, Mystique should have a significant agility edge over him. Her entire fighting style is based on being fluid, slipped through enemy grasps, sliding on the ground, flipping through the air, etc.
She also has rather impressive pain tolerance. She took a stab to the gut and laid on the ground for quite awhile before being rescued... and she was conscious enough to shapeshift into a security guard while in that state.
He's not a healer, she'd have to be actually strong enough to apply the needed force. What strength feats does she have to be snapping Nobu's neck?
She's strong enough to do it, casually, with her feet. She is strong enough to deliver kicks which could knock Wolverine back (including blows to the head. His skull could take blows which only hurt the attacker's fists; that didn't happen here).
There's also this. Multiple good feats:
0:02: Flips, knocking back three soldiers (two stepped back).
0:06: Picks up and throws a soldier an impressive distance.
Throughout: fights in a room surrounded by soldiers without getting tagged by bullets.