One thing to note is that the underground lakes are all contained. Every local map tile has its own self-contained cavern system, and they don't connect to ones from other map tiles unless there's an underground road/tunnel because of the way that caverns are formed relative to height above the lowest point in a local map tile. Unless something changed in an update since the last time I checked (which, granted, was a few years ago), if you embark on the edge of a local map tile, you'll find no lakes or passages that head past the edge of the local map tile.
Boats and multitile ships - aboveground and belowground - are planned already, I believe. I remember reading talk in Future of the Fortress years ago about how it was trouble working out how a ship turning would shift all the creatures and objects onboard to fit new orientations, for example.
Once we have ships, I'm sure we'll have seafaring trade, as that's one of the three most obvious things to do with ships in a game about adventure alongside discover new lands and piracy. It'd be cool to have the ability to send dwarves out to sea on missions including trade missions, both aboveground and below, although below would run into the technical problem of lakes not actually connecting underground, and you'd wind up with something like dwarves having to carry their boats with them over the land parts, which would seriously crimp their cargo capacity.
(Also, gears aren't necessarily "clockwork". Clocks in those days had to be made with water clocks, which isn't really different from what we have in DF now...)