Speed over water, speed over land - who cares? It's all the same, right?

If you're riding over completely still water with no waves or currents, yes.

But, most people ride on lakes or rivers that have water movement. Even closed-in lakes can have surface currents caused by wind. With a GPS-based system, if you're going against a 2 MPH current, you'll be going 2 MPH too fast, and when you turn around you'll be going 2 MPH too slow. That's a pretty significant 4 MPH difference.