I believe what is meant by "dark water" refers to the deep ocean. It's that point where the sea bottom drops away completely and it is no longer possible to dive deep enough to even reach the bottom with unlimited breath. There is a distinct color change at that boundary, where the water turns much darker than it is inshore. Beyond this point, there are no creatures, not even fish, and players that swim out that far from shore begin to suffer fatigue.
This is just all conjecture based on observation, but it makes sense to me. Then again, game programmers sometimes use labels that are counter-intuitive.
This water-mesh you're referring to and what depth it needs to have established...
It seems you're saying the height used will determine if any water is passable by any creature. Wouldn't this instead mean you'd need to use the largest creature's height? This means anything shorter than that measure would have to swim across. This would solve the issue of very shallow water, wouldn't it? Since the water navmesh would lie below ground level at those places, any creature could then walk, wade, or swim across as needed.
Or am I still not getting it?