Yes, they did build fleets on lakes. I'm sure the Caspian sea would be a reasonable place for some fleets too, and commerce. Movement of goods by ship is infinitely cheaper than the alternatives at the time. And even today. The problem with EU3 is a bad algorithm for allocating resources and famously failing to use manpower as a natural constraint in production in favor of gamey and arbitrary kluges.
Well, ok, lakes are a pretty minor issue. But remember that the map is not the terrain.
It may be that the game severely underestimates the populations of the Americas and we need a plague event that may, or may not do the historical reduction, based on the lucky contact. Given a few alternative events, the Americas could give a good show against the Europeans and, maybe, to the extent that they infect and colonize the East.
Silliness aside, the Americas need some rethinking.