When Superman is flying through the ocean to stop a torpedo, the sound effect is the same "whoosh" as when he flies through the air. There would be no sound at all if he was flying underwater.
The submarine crewmen are able to hear Superman speak from the outside when he's talking to them (as they look at him in the periscope), even though submarines do not have a hearing device for people to hear what's on the outside. However, Superman has special super powers, it's likely he was using one to 'project' his voice to the crewmen.