Take an leaf from (historical) fiction

Das Boat's convoy attack is a good example of a submarine fight. The book is very good too. You could easily adapt this to a space opera setting. The Master and Commander film (and book) are another good example where ship-to-ship combat. Finally, Midway is a great film focusing on both the air and naval sides of the battle. Space opera generally tend to see space as either submarine warfare (The Expanse) or glorified air plane combat (Cowboy Bebop, Star Wars). Of course, all of them take their inspiration for real life™. You could do that too: Raid on the Medway for example.

So, do what these guys do: use limited information to build tension, raise the stakes, and then explode in a fast ball of fire! Repeat.

Why the battle matters?

The game should be about the player characters, so that is where your focus should go. Ships blowing up are good special effects that can be seen but rarely interacted with.

Why are the players there?

What are they trying to achieve?

Once you have an answer to that, you can make combat more interesting by focusing on what the players do, not the ships. It is the hundred of small decisions in the middle of the battle that matters: Do we support ship X or attack ship Z? Do we keep firing on ship A to sink it, or do we allow it to flee? Do we move to intercept T or just fire some torpedoes? Do we try to disengage or keep close to their capital ship? How are we dealing with damage to the ship?

Finally, combat takes a long time (hours/days), which is generally not modelled well by RPG systems: so use more descriptions rather than tactical info dumps. You can, of course, focus the action from time to time where critical events happen.

There are no such published mechanics. That means it's time to improvise.

So what you have here is a unique encounter. That's great! Those can be a lot of fun, but they require a bit of improvisation.

First, figure out what rules do apply. You know that the underwater fighting rules apply. You know that the AC is 15, and no hit that deals less than 15 damage is going to matter at all. Okay. Cool. Now figure out how you want the encounter to play out for the characters. It sounds like you're aiming for a stealth encounter of sorts, so you're going to want to figure out what things can alert the crew, what things might draw other attention, and what the crew and/or other attention can do about it. Just as a rough example...

• Give the ship some number of "flood points". This indicates how much water it can take on before it sinks.
• Have some function by which damage done to the hull translates to flood points per round.
• Have something about how dealing damage to the ship in various ways can alert the crew (from the smashing noises). You can go into as much or as little detail as you want to here - either different parts of the crew get alerted at different times or they all get alerted at once or whatever. Similarly, various amounts of flooding would be likely to alert the crew (they'll notice that the ship is sinking) and possibly some other stuff.
• Figure out what the crew can do to try to thwart the PCs once alerted. (like, say pumping out water, trying to fix the holes, trying to attack, calling for help, moving the boat, or whatever). Put in some rules for those things.
• Figure out if there are any sea critters nearby that might be attracted to the noise and need to be fought off (which might make its own noise).

...something like that. You can make it more or less complicated and more or less challenging as you like depending on how much of a big deal you want this to be, and what kind of an encounter would work well with your players. When you're figuring out levels of challenging, remember that the first challenge is going to be dealing at least 15 damage while flailing about underwater in the first place. Also, as always, try to make sure that everyone who comes along on this underwater adventure has at least something useful they can do.