Did some testing with it.
Targeting enemy radardot (surface target) while being in water: Doesn't work.
Com walks towards the target but never fires.
Targeting sea surface or identified but jammed target (ghost image) while being in water:
Doesn't work. Com walks towards the target but never fires.
Targeting land from water:
Doesn't work. Com raises his arm as if to fire but never fires.
Targeting water from land: Works.
I don't know if thats intended or a bug tbh, but it would be nice if it worked cuz it'd enable another possible com morph for sea:
The Tacnuke-sub for poor people commander.
1600 metal cost, 700 base range, 1500 base dmg - but free missiles.
Not enough to efficently kill land bases or enemy combat units, but enough to wreck stationary stuff.
Currently sea coms are even less effective than land coms.