Can anyone direct me to where in the rule text it states that APT's bypass the shields? I know they do but why isn't this stated explicitly on the card? What other upgrades are similarly not defined clearly? Thanks

It is specified by stating that you draw a damage card instead of just taking a damage.

Veiv,

The card reads "Black critical: Deal 1 faceup damage card to the defender. "

The card itself states why it can bypass shields.

If a black die hit/crit is still in the attack pool by the resolve damage step, the attacker can choose to trigger that upgrade cards ability.

After that, all damage is then taken, one at a time, starting with any shields on the defending hull zone, and then any remaining damage taken as face down damage cards.

This video may help as well.

As for other cards, there are many that can change or effect a game then what is otherwise considered the "norm".

That's the benefit of equipping upgrade cards.

Cool got it; thanks all