Alex
I'm no expert, but I find your point very interesting and will explain you how I think it's working:
I use a D200 with a SB800 Strobe.
*) In the custom settings menu of the D200, I set "Flash Sync speed"
- at 1/250 (than the camera won't allow you to go faster than 1/250), but it will allow you to go faster than 1/60 up to 1/250.
pm. You have also 1/250 FP (for Focal Plane, a technique for better synchronisation of the flash with the movement of the shutter curtains), if this is supported by your flash than the flash will synchronise with faster shutter speeds than the flash synchronisation speed. I do not chose this option, as I don't see -yet:) - the advantages for UW photography, and it avoids me choosing to fast speeds when UW.
**) You have another menu to set the "Slowest speed when using flash". I set this one at 1/60
I set the flash on TTL.
Now:
In P and A mode, the camera will set the shutter speed, between 1/60 and 1/250 (depending on the ambient light). As underwater we generally don't have so much light, always 1/60
In S mode, you can set any shutter speed up to 1/250. The camera set's the apparture according to ambient light (for macro a bad UW choice; as lens to open for DOF).
In M mode, you can nicely choose your shutter speed (up to 1/250) and arrange the aparture, in function of the ambient light you want, TTL takes care of the lightning of the foreground. So I thinks this is the way to go.
I've used myself so far always 1/60 but I notice that for some species this gives a blurred effect. I wonder if they might see the pre-flash TTL burst, start moving, and ... unsharp picture. I'm going to experiment with the shutter speeds 
rgds
Sven.