Okay ! I got a shinobi in my game and i guess he will want to assassinate some people and i was asking my self. If he sneak passe somebody notice with a fitness check (air) for sneaking pass them and he then do an attack. Do I considere is attack as an automatical crit cause the personne didn't have the oportunity to defend or I say they still defend as usual cause it would be reflexe at this point ?

It depends on the situation.

Against generic minion NPCs, I would suggest not even considering it a conflict scene; there was an old example in the beta rulebook in the skills section:

"Stealthily dispatching a single Minion NPC guard outside of a conflict scene without alerting others: TN 3 Martial Arts [Melee] (Air) check"

I'd pretty much resolve the roll against the unlucky henchman as that.

If it's actually someone, or your target, then I'd use the full-blown conflict scene rules, and whilst I'd almost certainly give you first go (because you'd be using your focus to their vigilance and you're a - presumably Air-heavy shinobi), I would still allow them to defend. You probably wouldn't have a hard time creating situational disadvantages for them, though.

no, there are actual school abilities that tie into this. so it shouldn't be automatic. the only way its automatic is if they are incapacitated or unconscious. I would say its fair to not allow the target to soak with fatigue, only armor, or perhaps soak fatigue equal to vigilance? but really, if you're assasinating, it shouldnt be a strike. It should be a skill action with a poisoned or assasins weapon.

Per the rules, Sneak Attacks wre governed by the initiative rules: Ther shinobi will roll initiative with his focus, the enemy with vigilance, which is less.
So the shinobi will probably act first. He does not get further advantages from his surprise attack, though.
That's what techniques are for, in this case the Veiled Menace Style kata, for example.

If your player feels that that is unfair, remind him that the rules count for foes as well.
Would he like to take an automatical crit from every minion that surprises his character, as well?