What I believe I'm going to do is give the players choice as to how they deal with ships
My Idea would be to give sea vehicles their own stats and levels based on their destructive potential, craftmanship, size and how use to PC's are to using a certain type or individual boat

In other words, Levels reflect on how much of a risk it is to fight them rather than just a complete reflection of how many ships an enemy has grinded through
As for Ship specific weapons, I would like everything a ship could use to be classed as an Imporived weapon and that what happens to the ship isn't determined by the overall hp but on whether it gets blown to bits or not

It's ok to have a lot of holes in your ship so long as it isn't sinking

However, players would recieve debuffs or be limited in some way based on damage, for example, if there's a hole in the deck, that would be classed as Dangeous terrain or become an obstackle that would have to be jumped over
And at the core of it, it'll be like having a level 1 character fighting another level 1 character so you'll just be trying to shoot the enemy and you'll be checking to see if things hit or if said bolder yo have catapulted has managed to smash through wood
Last of all is the subject of loot

I've decided that if you completely destroy the enemy ship and it sinks, it would up to you if you want to try and recover some of it

If loot gets burned up because some wizard likes fireballs, tough. If you're diving down for gold, you would have to make a Strength + Dex check vs the weight of yourself and the thing you are trying to pull out of the water

of course water currents and your ability to swim would also come into this
