Not by promotions. That would make the promotion tree that focus on anti-naval useless in many situations. I was thinking more of siege units not having penalties against naval, and field promotions are just good against units, so a field promoted cannon should handle caravels better than ranged units. And it makes sense. If you want to sink a ship, you throw big cannonballs, not light ammunition. Remember those fortified castles in the caribbean? They were equipped with cannons for dealing with invading navies.