Subs have the following advantages when enemy Destroyers are NOT present:
1. They can’t be attacked by Air.
2. Their attack’s hits resolve before non-Sub units roll.
3. On Offense, they may submerge once they’ve completed their attack, before the other side can return fire
4. On Defense, they may submerge before being attacked at all.
Note that Subs also have the disadvantage that they do not block sea zones, you can have 1000 subs in a sea zone and the opponent can still move a transport through it.
On the other hand, without Destroyers, you can’t destroy Subs unless the owner chooses to let them participate in combat.
Oh, and ogrebait, Destroyers cost 2 more IPCs than a Sub, meaning that Destroyers cost 33% more than Subs, which adds up to the point that 3 Destroyers only beats 4 Subs 55% of the time when they are the ones attacking, meaning that the Subs are defending at a 1 with no special powers.