It sounds neat to do, but it doesn't work (water roads). First, the AI doesn't use the water workers, because you can't flag any naval units with the terraform ability (even though you can flag the worker jobs). Second, and most interesting, is that once you build just one tile of sea road, harbors completely stop working in the game. It is very strange. From then on, you have to connect all cities with roads or airports in order to have trade routes. Also, IIRC, sea roads when built do allow you to connect your cities to sea-based luxury and strategic resources.
The invasion of sea cities works the same as invading a city built on a 1-tile island. It requires units with the amphibious assault ability. But the AI won't use sea settlers (again, because naval units can't have the right flags checked), so the question is moot. There are a lot of cool things you can do in the editor that the AI can't use. My favorite are planes with the immobile flag unchecked have the ability to move over land or water, but the AI won't ever take them onto the water.
If you are making an MP-only scenario, then go ahead and do all kinds of crazy things, just make sure that all players understand the special features of units.