There is no counter system. It’s just spam as many ships as you can to win. There is supposed to be a system involving buildings and some artillery, but it is minimal and can be avoided by staying out at sea. What we need is ship roles that are actually differentiated such as ships that fight in melee.
Better maps would also help. Hybrid maps with a chokepoint would actually let naval units be pivotal in participating in battles or bypassing a congested land route.