The AI will build harbors and boats but it is not, IMO, very good at it yet. This is something that will take quite a bit of time for it to master because I'm requiring the AI not to cheat so it has to first build the transport, load the transport, send the transport and find a beach to land on (it's not like Civ where you can just build a boat on any water adjacent tile nor is it like HOMM where units just turn into boats and walk across the water).
So you will occasionally see the AI build transports and send them out but it's not very good at invading yet or colonizing yet.
Okay, we are looking forward to get improved AI which will handle harbors better and so getting more types of maps available (islands, multi-continents etc.). I'm sure it will be done.
But I'm wondering why there isn't any river on "random" maps. Is this another feature which makes difficulty for AI?