So the Net effect in the end is:
If the Ship has No Shields on that Zone at the Start of the Attack: One Face up from the APT Crit effect, Two Face Down from 2 Damage Points.
If the Ship has One Shield on that Zone at the start of the Attack: Once Face Up from the APT Crit effect, One Face Down Card, and the Shield Removed.
If the Ship has 2+ shields on that Zone at the start of the attack: One Face Up card from the Crit effect, and the Shields Depleted by 2 Points.
So no matter how many shields a ship has. APT will deal a face up card if I read this correct. With a roll of a Crit. That is not how I was playing it but this is cool.