Right, but I think the ship is not a hulk when it takes the damage from the crit.
If you're shooting at a ship and reduce it to zero hits only by shooting itself, and inflict in addition to it a crit that causes extra damage, you still roll only once for catastrophic damage, not twice, because it's not a hulk when it takes the extra damage but still a badly damaged ship. Excessive damage taken by a ship expires. It's basically the same situation as in a boardnig action.