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Now if you are playing a large game and are running out of cards you can always shuffle the discarded cards (from destroyed ships or abilities such as determination) and make a new deck. However the rule goes if the card deck is completely exhausted then every critical hit is treated as a direct hit.
The situations where one would deplete the damage deck and not have a discard pile to create a new one should be extremely rare. Now maybe I missed it but my impression was that if there are no cards to draw then a crit result is just treated as a NORMAL hit which is represented by some token; to put it another way if there are no cards to draw then there is nothing special to worry about from critical hits anymore.
The only time I'd really advocate for using counters/tokens to represent unknown damage cards is when there is a real danger of actually running out of damage cards. How does that happen? Maybe some epic games and having both sides share a single deck could also cause it but if it happens in a normal game I'd say someone isn't playing too well if they are allowing that many ships to run around with that much damage on them. Six TIE Bombers could carry 31 damage cards on them (a hull upgrade in there somewhere) with each of them one hit away from death but even this leaves you with enough cards to finish them off and rebuild the deck.