The knowledge for this comes from the ninja's understanding of ki, a mystical force. It's also available far earlier than Crippling Strike. So (Su) makes sense to me.
The (Su) means it's magical in some way, and since the ninja is all about ki, I don't think it's a bad assumption to link the two.
For those curious:
A ninja with this trick can strike at an opponent’s vital pressure points, causing weakness and intense pain. Whenever the ninja deals sneak attack damage, she also deals 1 point of Strength or Dexterity damage, decided by the ninja. Unlike normal ability damage, this damage can be healed by a DC 15 Heal check. Each successful check heals 1 point of damage caused by this trick. A ninja with this trick receives a +10 insight bonus on this Heal check.
A rogue with this ability can sneak attack opponents with such precision that her blows weaken and hamper them. An opponent damaged by one of her sneak attacks also takes 2 points of Strength damage.
Pressure points is available as a base Ninja Trick, while Crippling Strike is an advanced rogue talent.
If there weren't other ninja tricks that were (Su) but didn't use up ki, I'd agree that it's most likely in error. But due to Wall Climber being (Su) for the ninja, I think them both being in error are unlikely.
I can't give a great explanation of what about pressure points is supernatural, although it's possible that it's some sort of magic that saps the strength of an enemy, or that the pain is amplified through magic.
Can they both be used at the same time for a total of 3 / successful sneak attack?
No...abilities with a * mean you can only apply one to each sneak attack