I've found a kludge that allows the effect of an underwater road or avenue tunnel between cities. It's a bit of a cheat, but it does the job.
Requires: RushHour and NAM.
1. Use your preferred means of draining the water (I like to slap the NAM Diagonal Bridges folder into the Plugins, because it's handy). Fire up SC4.
2. On what used to be the sea bed, draw a short connection to the neighboring region (road or avenue).
3. Using FLUPs, make a tunnel from right near that connection to wherever you want your land-based tunnel portal to be. Do likewise in the neighbouring city.
4. Exit the game, remove your water-drain hack, then fire up SC4 again.
That city connection (and the FLUP portal next to it) are now underwater... but they still work. So what you get is the effect of an underwater tunnel to your neighbouring city. Works best if your city edge is 100 meters or more underwater (so that the underwater FLUP and connection aren't seen through the water). Very handy for connecting island cities.
It's a kludge, I know. But needs must when the devil drives. :)
(https://www.sc4devotion.com/forums/proxy.php?request=http%3A%2F%2Fjessilaurn.com%2FSC4%2Funt.png&hash=124e763f30db019974119a4218ebd9069646cdf2)