So on a card like assault proton torpedoes or some of the ion cards when it has an effect that is triggered by a critical does that mean that the critical dice is spent and does not then count towards the damage number?

No. The critical icon still gives you a damage; it also triggers the critical effect. This is the case for the default critical too: deal the first damage card dealt face up.

RRG pg 4 Critical Effects for more detail.