Fore section blows up. It had a critical damage reducing it's primary weapon value by 2. Does this critical still apply thereby reducing it's primary value to 0?

Doesn't seem to be anything in the Huge Ship Rules to suggest you do anything with the cards until the whole ship is destroyed, so yes, I think it would.

Better hope you had a good weapon loaded on the aft section.

yea. both questions (that you've responded to) both happened tonight. I didn't read the rules carefully enough for the other one and let my 11-year-old jam my small ships to pieces but then, like you said, told him that it doesn't talk about the damage cards so his primary on his tantive was 0. thanks for the input!