Hi there,
I'm sure this is a bug and not intended game behavior.
https://replay.faforever.com/15249354
In this replay, at 30:30(ish), the grey commander is getting torpedoed. He gets on an air transport while torpedoes are incoming. The torpedoes pursue him out of the water, hit him while he's in the transport, dropping him back dow, killing him shortly after.
I'm sure torpedoes aren't supposed to be able to leave the water.