The Enclosed vehicle trait says crew and passengers cannot be specifically targeted by those outside the vehicle unless there is a particularly good reason.

Eye of Vengeance allows a character to add his degrees of success to the penetration for a hit.

Armor for a vehicle acts as normal armor, there is no 'scaling' so, would you all allow someone to shoot someone inside an Enclosed vehicle using Eye of Vengeance, rather than having to damage the vehicle and hope that they can deal enough damage to allow them to damage crew?

I'd say you can't target the people inside, apply it to the vehicle's armour. Now, a Called Shot to a window or something? That might be another story.

No. You just get more penetration on the vehicle. You cannot target the people inside because you cannot see them.