Just played my first game with a Transport on each side. This question occurred to me: if you have two transports in the same squad do you need two sets of damage decks, or do they share one? I didn't see anything in the rules one way or another.

I think each ship should have its own damage deck. I don't, however, have any solid evidence to back that up.

Nice question. For the moment, I'd also use both damage decks, one for each transport, until further clarification from FFG.

Seems the most logical way to me.

The rules for huge ships imply, but don't outright say, that each ship should have its own pair of damage cards. This is backed up by the fact that the damage decks are different for different types of huge ships.

So yes, each huge ship has its own pair of damage decks.

Individual decks sounds right to me, if only from the practical side of things. With 8 hull and only 10 cards in each deck, it would be very easy to exhaust a shared deck.