I think the main problem is that submerged units are not balanced around tanky units that can fight back.
Arguably the tankiest practical submerged unit is the Scallop and that only has 1200 health.
If you add a commander weapon that can fire submerged, you basically open up a whole can of worms.
You can now have a long range underwater sniper com with a huge HP pool. There is no comparable unit to that and sea combat would likely revolve around submerged long range sniper coms.
There used to be a long range sniper sub and it got removed because it was considered degenerate artillery gameplay.
Personally I didn't think it was that degenerate because I like arty duels unlike most players.
Now the longest practical submerged range is also the Scallop with 270 range, so even just a commander with 300 range could be considered a sniper/artillery if it could fire underwater.
Now you can argue that Ultimatum is more tanky than a Scallop, but it has less range and is easily overrun by raiders and the cloak is ignored by sonar.
Oh, and also the Detriment is more tanky and the gauss cannons have longer range than Scallop, but yeah...
Maps are rarely deep enough for Detriment to be fully submerged and it is in a whole other class anyway.
