But you can pay the cost. You can still suffer two damage, it just so happens that two damage is more than it will take to destroy your ship.
Here's another angle to consider. What if the ship Vader is on has suffered damage equal to its hull value minus two. Activating Vader's ability will still destroy the ship, so can he do it? Obviously yes. So what difference does it make if the ship has received one more damage card? It still suffers two damage, it is just destroyed after the first one.
Being destroyed after the first one means the ship is out of play, and cannot suffer the second damage. So no, you cannot suffer 2 damage if you only have one hull remaining.
But you never have one hull remaining. You are destroyed when the number of damage cards equals or exceeds the hull value of the ship, not when your hull value reaches zero. If your ship has five hull and you have four damage cards, you don't have one hull left, you have four damage cards. If you suffer two more damage, you are destroyed after the first one is assigned, but you still suffer the two damage. That's why it says "equals or exceeds". If it worked the way you said, damage could never exceed the number of hull because the ship would be destroyed at the point where the damage cards equaled the hull value. Even your example of drawing Direct hit wouldn't do it, because the ship would be destroyed after the first point and wouldn't be around to suffer the second.