The sidebar on page 20 of the Second Edition European Rulebook states:
In a sea battle, if the defender has only transports remaining and the attacker still has units capable of attacking, the defending transports are all destroyed, along with their cargo. You don’t have to continue rolling dice until all the transports receive hits. This will speed up combats. This also occurs if the only combat units remaining can’t hit each other. For example, if the defender has only transports and submarines remaining, and the attacker has only air units remaining, the air units and submarines can’t hit each other, so the transports are defenseless.
The example is reversed but it still applies here.
You don’t have to fire for each transport because the outcome will be the same. It’s just a matter of time before you roll the required numbers to hit each transport. The only time it does matter is if the transports are with an attacking force, because the transports have the option of retreating.