Waypoint pathfinding for diver units (while they are underwater) is broken in at least 2 ways. Firstly, the divers do not always follow the most direct path to the waypoint destination. Often times they will veer off course and end up clipping through land/buildings and take a very roundabout way to get to their destination. This seems to depend on the dive team's location and their destination, as well as what is in between them and their destination.
Secondly, setting the combat mode to "STEALTH" results in divers moving extremely slowly underwater. Divers will move a few feet, then stop for 5 or so seconds before moving a few feet again.
Also, while underwater, it seems the waypoint's SPEED property is ignored. AI divers always seem to move at a "walking" speed while underwater.