Here's a possibility... When your cv group is in range (horizon distance) of an enemy task group a sub would appear in the friendly task group. At that point, the sub would become useable. That would solve the tedious work of hunting with one, and it'd also give an indicator that the friendly group is getting close to a not so friendly group.
One thing to remember, the enemy group has a sub at that point as well, promoting sub vs sub combat. If the cv is killed, or moves beyond a certain range of the enemy task group, the sub would warn the players driving the sub that the sub is going back to running quiet (de-spawning) and would disappear from the group as a manable ship.
EDIT: This would also solve the "why are there 30 subs running around doing nothing" problem that would happen if individual users can up a sub at any time.