I'm far from a competitive master but a part of me is very not surprised to hear Hunter spam is the sea meta because it's a functional cost effective answer to nearly every other type of unit ships are expected to match up against. Hunter beats Seawolves, Hunters beat hunters. Hunters beat nearly every amphbot. Hunters beat most hovers it feels like. At its worst it feels rather 'neutral' in most exchanges that you would expect it to hold any weight in.
Going into why, the first layer is pretty obvious: Torpedoes are awesome in the water. They don't really have problems firing past each other in mass because torpedoes do have some parallel to 'lob' or indirect fire, with the bonus of also being homing. Now take that skirmisher style massability, and put it on a unit with raider speed and damage, and you have a very potent unit. It's a bit on the frail side, but it does make a strong core.
I'm actually surprised to hear the Seawolf isn't more popular considering it's effectively about double the stats for double the price with the bonus of forcing your opponent into things like Hunters, which I'd figure Seawolves generally beat in a 'brawl', especially if you catch them before they can get the siren or two out that punishes a Seawolf pack with sheer aoe power.
The Corsair not performing well makes sense as it has a lot of overlap with the hunter at the expense of only hitting above water, and leaving yourself vulnerable to subs is just a recipe for disaster. Mistral always seemed like a niche unit that weighs in as a 'cheap early shore bombardier' for when you're not quite at Envoy stage. Neither the Envoy or Mistral seem to feel 'good' in dedicated ocean warfare though. The siren does a good job of being the 'go to big thing' as an assault, but easily overshadows Corsair in the Riot role if you're trying to make a screen for a back line, and even contributes to that back line/skirmisher position, while also still being a solid riot, and assault.
So kind of flipping through the Shipyard roster, it seems like it comes off as having 2 generalists that check a few too many boxes too efficiently, and then the rest of the roster just kinda, lacks effective identity and seems to only shine in a few niche cases. Corsair's are really chunky for their speed and deal lots of damage, but lack true aoe like a riot, and can't target the main things I'd want a water riot to be screening for of sneaky underwater snipes. Mistral sure, exists, but waiting until you can get an Envoy, or just stride out shoguns is likely what you're going to really want to look towards for long term siege. In the short term, Sirens can harass and, with focus fire, snipe priority targets every so often, while being fantastic front line bruisers.
Is this a problem? I don't know. Kind of yes, kind of no. Balance in Zero K is wonky as all get out, and super convoluted due to each factory interacting with other factories and different environments and map types. Shipyard units only exist on the water, and need to be balanced around this relatively featureless terrain type's limitations. Most maps, water is used as a form of natural barrier to be tested, taking up very little space overall but placed tactfully to create natural choke points in terms of movement, but making dynamic strategies in that not all factories are affected by that penalty the same way. Ships try to take this area that is generally considered disadvantageous, and thrive in it. Going ships on a mixed terrain map is a -statement-, and that statement should be rewarded in ruling that terrain. You then are sacrificing power when it comes to leaving it, especially compared to the other hydro factories.
How do you balance that on all water? That gets more difficult because most water terrain is flat. Adding islands gives some more wiggle room for the hybrid factories to flex their strengths; shallows, sand bars, and cliffy islands filling a similar niche as an inverse to a river, shallow, or lake would on a land map, but even the nuance of 'slightly hilly terrain' or 'high vs. low' terrain is lost on the water. One small idea my brain has toyed with is different types of water, something like 'rapids/currents', or 'deep sea' or 'stormy'. I'm not sure how that could be implemented exactly in Zero K, if it could be at all, but the lack of dynamics in water itself, cause water is water is water, when compared to land, which has highs, lows, smooth, hillty, jagged, etc. Is a substantial part of why the tool kit that could be brought to the water is so small scale.
The OC's original idea of making a 'Rover' equivelant to the Shipyards 'Tank' is a neat starting point though, even if it would be a large undertaking, it's not unfounded. Another idea that may loosely be considered is maybe a 'Shield' shipyard, or splitting the current shipyard to a more dedicated 'submarine yard' (as a cloackbot parallel) and 'flotilla' yard, but that's quick and loose conjecture and spitballing. I've definitely hit the ramble point in this so I'm just going to call it here.