I believe that for this we must allow small boats such as canoes and fishing boats to move through shallow waters. Big boats would reduce ralism, but small boats would be fine. Fishing Boats, Canoes, and Catamarans should be able to cross shallows
I also think that it is already possible to build on the water, for example in the indochina map you can build on the lower parts of the river, so in theory a map like this is already possible.