When dealing with a lot of small vessels, I borrowed from the EotE game a bit and added in structure and breach for vehicles and vehicle weapons. For each point of structure a building/vehicle has, it has DR10, for each point of breach a weapon has, it ignores 1 point of structure.
So the rogue fires his crossbow at the ship with structure 4, it ignores the first 40 points of damage he does.
A ram from the prow of a ship might only do 3d10 damage (as a person just bounces out the way) but it has breach 5, so will hit the skiff for full damage.
The small fire-thrower on your skiffs prow does 3d10 damage, but against wooden structures it has breach 4, so will hurt most structures pretty badly.
The good thing about this are:
- It lets vehicle weapons matter, without making them auto-death to combatants.
- It does not overshadow the damage that a DPR class will put out like giving everybody a cannon to fire normally does.
- It also addresses the silliness of stabbing a ship with a rapier and expecting it to wittle the ship down in a meaningful way.
- It allows you to have small HP pools on ships, without fear of PCs just stabbing them to death. This stops overly protacted combats. One good shot from a siege weapon will destroy a small ship, but it would take PCs with a sword ages to do so.
I gave great axes and mauls breach 1, this made them the right tools for the job when attempting demolition of enemy rudders etc. I set breach 1 as the benchmark of an unremarkable wooden door, so an axe is not getting through a proper palisade any time soon.