That is some awesome idea right there! I fear this can only be addressed post-release, because it is a really hefty piece of programming.
But, nonetheless, some ideas:
Claiming, binding and capture
If possible at all, the smallest vessels would need to be claimed like a coop to be usable, an the larger ones would have binding slots just like houses or, even better, the coming siege tents. If the whole crew is slaughtered, all slots should be emptied, so the enemy could capture and use the ship.
Battle and damage model
To destroy or damage a ship, you would need to use the ram of another warship for medium damage, siege weaponry (either from the shore or a capital warship) for high damage, and fire arrows/naphtha grenades for low damage, but the chance to light it on fire.
This could be implemented in the carpentry skill and would need to be divided into stages:
The first stage would be the hull. The hull itself would be crafted like a piece of furniture and would, once completed, have the same properties as the building sites of structures. Then a tailor needs to craft a sail from rope and cloth (tailoring lvl 60), which then should be dropped into the hull and be "hammered in" to craft the final vessel.
For progression and ship types
, i propose something like this:
lvl 60 small vessels like canoes/rowboats
, requiring some boards, nails and/or bone glue, and a pair of oars (crafted with the knife from a billet, carpentry lvl 0), these could be equipped on the respective sailor like a hammer or so. High speed, almost no combat capabilities except boarding.
lvl 70 a medium sized fishing boat
with sails for 4 sailors, requiring boards, nails, and building logs in the first stage, and sails in the second. To use that boat, a character would have to be at least lvl 60 in fishing hunting and have a net (from rope, required tailoring lvl 30) equipped. Low to medium speed, almost no combat capabilities except boarding.
lvl 80 a small warship,
e.g. some kind of viking-like longboat
for up to 7 sailors and armed with a ram - the sailors could of course board an enemy vessel or shoot with bows/crossbows if so desired - requiring boards, nails, bone glue and building logs in the first stage, the hull, then rope, sails and common ingots (the ram) in the second stage.; For rowing and a ram attack, the sailors would need to have oars equipped. Medium speed when under sail, high speed when rowed.
Too at lvl 80 a small cargo ship
(program-wise a floating small warehouse, i would say) for 6 sailors and built from the same materials as the warship, but with door modules instead of common ingots for the cargo bays. Low to medium speed, almost no combat capabilities except boarding, but higher defensive potential than a fisherman due to higher HP and better crew defense (higher railing, for example. As a special ability, this ship could be rowed AND sailed for a short period of time like the "FLEE!" ability - very high speed! At sea, this needs to be longer than ashore, like 10 minutes.
lvl 90 a medium warship
, e.g. a galley
for up to 12 sailors, which is built and used like the small warship, but is more capable, like having a hoarding or similar. A slot could be added for a warfare engineer, who could use siege ladders for boarding. Medium speed, but lower than the small warship.
lvl 100 a capital warship or galleon
for 20 sailors and 2 warfare engineers, armed with siege weaponry like trebuchets, requiring the first two stages like the others, and the parts for the trebuchets in the third. Low speed, exceptional combat performance, due to boarding defenses, hoardings, trebuchets and high number of boarding personnel.
Too at lvl 100 a capital merchant ship
(a floating large warehouse) for 12 sailors, muchmore durable than the small one and with added defensive capabilities like hoardings and boiling oil for close quarters (boarding defense and chance of setting the enemy on fire)
Balance and battle performance
Balance-wise I would thus conclude, that
a capital warship in a 1v1-battle, can defeat any other ship, if not caught by surprise (at night, for example) and boarded;
a medium warship could defeat any smaller ship, but would be evenly matched against a capital merchant.
a capital merchant should not be preyed upon by anything smaller than a medium warship.
a small cargo ship can not defeat a small warship, but can outrun it for an hour or so (depending on mechanics like cooldown etc.), so it becomes very time-consuming to hunt down when it is competently sailed, giving the crew the possibility to seek shelter in a harbor or call in reinforcements.
Fishermen need to stay close to shore, unless being guarded by a warship (I'm thinking of fishing fleets here, just like mining fleets in EVE Online). To give an incentive to use them anyway, i support the ideas from ape21675 and Mortdecai, especially whaling is a genius idea!