I think the root of the problem is that water is very inconsistent and poorly designed in this game. There are about 10 different types of water in the game and you cannot distinguish between them in any way other than trial and error. Mapmakers have a huge amount of responsibility to design their maps to have clear and consistent mechanics, but 99% of them aren't even aware of this and just try to make pretty maps. You can never create good balance and clear consistent mechanics under these circumstances.
The only consistent mechanic shared by all water is that hover units can go over it and amphibious units through it as long as there isn't a cliff blocking them (which can also be unclear).
Otherwise, water always has these unknowns:
- Is it deep enough to protect unit X from surface fire?
- Is it deep enough for torpedos and depth charges to work?
- Is it deep enough to build a navy factory?
- Is it deep enough for navy units to travel through?
- Is it deep enough to hide submerged unit X from AoE with radius Y?
- Will the seafloor kill my units if I drop them there?
- Can my amphibious units cross there or is there some underwater terrain issue?
If subs were capable of adjusting their depth like air units it would still never be clear if they are deep enough to be safe from AoE with radius X since the depth of the water can vary significantly. You don't want to make underwater units immune to all AoE just because they went 1 inch under the surface either because that is stupid and still inconsistent. You could make the AoE some sort of ellipsoid shape so it doesn't penetrate as deep into the water, but that doesn't address the issue, if anything it becomes less clear what can hit what. You could make water have a dampening effect (pun intended) so that damage taken from AoE is reduced with depth, still inconsistent and unclear. The way it currently is, where submerged units stay at a consistent depth at all times and take AoE damage if they are within range, is probably the most consistency you can get.
I think placing so much power and responsibility in the hands of the map makers is the biggest design flaw in Supreme Commander. It is the cause of this problem and several related problems which all have no solutions. When I was thinking about what I would want from a new Supreme Commander type of game this is the first thing I had to find a solution for.