It does not say an aircraft carrier has a combat value of 0. The carrier has an attack of 0 but it seems to still have a combat value nevertheless.
Look at the Pacific1940.2 rulebook, page 14. There it says:
Although they don’t have an attack value and aren’t represented on the
battle strip, carriers can still participate in an attack and can take hits,
as long at least 1 unit with an attack value attacks along with them. …
That should clarify the role of an Aircraft Carrier.
But your scenario is somehow independent from this. Here the rule says (from page 15, Transports section):
However, a transport is not allowed to offload land units for an amphibious assault in a sea zone containing 1 or more ignored enemy submarines unless at least 1 warship belonging to the attacking power is also present in the sea zone at the end of the Combat Move phase.
The carrier is a warship (regardless of its attack value) and the requirement for the transport being accompanied by a warship at the end of the Combat Move phase is fulfilled, too.
So nothing prevents the transport from unloading during Conduct Combat phase, here.
What the attacker can’t do is to attack the submarine, of course.