Without gunpowder, the shots don't make a loud bang or smoke, but the bullets themselves can pierce the wood and make noise.
Blackwake had really cool mechanics and a cool Captain menu to tell your crew what to do.
Some had to load the canons, others had to repair the canon holes. The sail had to be handled and much more. I think such gameplay would work with ball balists aswell.
The muskets and pistols could be replaced by crossbows, which should do a lot of damage on naked bodies. No seafarer wears armour, otherwise they cannot swim properly.
Ship combat in mortal is a very difficult endeavor, but not impossible either.