he subs do not have to be destroyed before the transport. Once the attacker can no longer hit the subs, ie. just air left the transports are toast as there are no longer units that can defend them. See page 19 in the manual. I think one of teh FAQs also cleared up the wording for the side bar that is on page 19 a bit as it says submerged submarines and air units.
This is from one of the FAQs that cleared up the poor wording.
Q. On page 29 it says that your aircraft may hit enemy submarines if you have a destroyer in the
sea zone, but it doesn’t say anywhere in the rules that aircraft can’t hit submarines without a
destroyer present. Do you always need a destroyer in a battle in order for your air units to hit
enemy subs?
A. Yes. Air units can only hit subs if there is a friendly destroyer on the battle board, otherwise hits made
by air units must be applied to units other than submarines. If you’re the attacker, destroyers in the same
sea zone belonging to your ally don’t count, since they’re not involved in the battle.