Um...Map Pack Spoiler Alert, sort of. 

I have sighted (on the map Dust Bowl) an AI transport, in water, with units on board. In later turns, it was gone. So yes, it moved units over the sea at least once.

In the same game, Gilden invaded one of of my custom Quendar opponents, and due to 1.) the serpentine land route required for land invasion and 2.) Me never see a single troop march along that route, and 3.) A landing spot right next to the first conquered city, I concluded that they did it by ferrying units across the sea.

That said, I have also seen the enemy AI park its transports on a beach and never move them. That was on Anthys, though, and there is much less to find in the sea than on Dustbowl. 

So my experience is by no means comprehensive, but my conclusion is that the AI makes at least half-assed use of transports, with intelligent use possible.

I highly recommend Dustbowl for using transports - ships have a lot of use on that map, and there's some very cool surprises waiting out at sea.  

After playing Dustbowl, I was a little disappointed by how little there is to find out at sea on Anthys. That said, I didn't have time to explore the whole sea, and there were still some goodies to find. 

On Wildlands, I seem to get my ass kicked every time, but I spotted lots of goodies I never reached out at sea.