I have never shot MF digital underwater, but I have shot a lot of medium format film underwater.
The main issue with medium format is that it is hard to realise the superior image quality of the sensor in most UW shooting conditions. Shooting through too much water significantly degrades image quality much faster than differences between sensors. There is a role for MF in very controlled conditions - such as pool or UW studio photography. But for wildlife/diving photography the disadvantages easily outweigh the advantages.
Finally the expert in UW MF... I've been waiting for you to chime in! B)
Here, from my seat in the darkroom (and if I read what you're saying correctly), I have to respectfully disagree about image quality degredation, especially with respect to the RMS values of film grain (or CCD noise) adding to silt "noise" -- That big piece of modern 2-electron film (such as Provia 400X or Pro800Z) gives you dead-quiet images.
Perhaps the biggest problem with medium format underwater is the lack of depth of field of the larger image size.
Is this due to the lower (50-100) ISO film you've been shooting, forcing you to open up your aperture, hence reducing DOF? If so, again the modern 2-electron films come to the rescue. And, since I can control the shooting EI and compensate (to a limited degree) by push processing in my processor, I can go even further than box speed. [For what it's worth, Fuji Pro 800Z pushes nicely to E.I. 1250 when the developer is 4:15 @100F; though much past that and the orange contrast mask gets pretty thick.]
Also, I'm spoiled: My goal is to tend more towards UW macro, like Michael ("Mickey") Maurer, as his Times Square exhibit 2 years ago got me interested in submerging my gear in the first place.
[Also, to a degree, I've been researching UW MF macro for Michael: I'm glad that your experience confirms my suggestion!]
From my experience this becomes very significant in the lighting conditions and subject sizes we typically work around underwater. Generally underwater we want our subjects as close as possible to the camera.
That makes sense, due to losses and color shift in the water...
For wide angle on medium format I often found that this would render the background out of focus - which did not look very nice.
Could you please elaborate on the focal length & f/stop settings you typically used? Would closing down the aperture & shooting a higher ISO film have helped? Could you post an example of this poor bokeh?
[For the definition of bokeh, Harold Merklinger has an excellent explanation with plenty of photos in "A Technical View of Bokeh," where describes what makes the out-of-focus images different for different lenses. Originally published in Photo Techniques magazine in the May/June 1997 issue. PDF.]
This may be less of a problem with digital backs. First because they are cropped therefore increasing the apparent DOF for a given subject repro size in the frame. And second because the large pixels size means that the ISO can be racked up more than on film, allowing the aperture to be stopped down.
You're quite right about the larger photosites vs noise; though the limit in practice is an ISO equivalent of 400 with most backs (though some, obviously, go higher). Answering James' point that CCD technology has been improving, the short answer is Yes. But, in practice with digibacks, the answer has been to pack more of the already-good pixels onto a given physical chip size (usually 36x48mm).
The other problem with medium format is lenses. Many medium format lenses do not focus close enough for underwater photography.
...And the ones that do are quite expensive (at least the Mamiya AF lenses).
But! Remember where I wrote that most MF shooters are professionals? Well, that means they know how to use extension rings to get up close. (Yes, you do lose a bit of light with the bellows factor; but with rings it can safely be ignored... Especially with TTL metering and TTL flash).
And the flip side to the advantages of the cropped MF sensor digital backs is that it further limits lens choice. The most commercial type of underwater shooting is wide angle, generally with fisheye lenses offering corner to corner 180 degrees.
To compensate for that, Mamiya just introduced a 28mm AF lens (102 degree angle on film, 94 degrees on MF back) to go along with their 35mm AF (90 degree angle) lens.
[As a point of departure, the 35mm lens on a 6x45 frame is the same field of view as a 22mm on a 35mm film frame; while the 28mm 6x45 is about equal to a 17.5mm Nikkor.]
Nobody earns much shooting macro! I am not aware of many medium format lenses that offer 180 degrees on a cropped MF digital back. Furthermore the autofocus performance of many MF cameras does not match that of the 35mm based systems...
Yeah, the Contax 645 AF mechanish was indeed a dawg... And they went tits-up, too. But, next time you're at a high end camera dealer (or make an excuse to come to B&H!
) try out the 645AFd-II's AF in the store. These AF lenses all have internal focus motors (more torque for faster twisting than with the AF tang on a Nikon); and the AF module is about twice as fast as on the 2002 model 645AFd (...which was twice as fast as the original 645AF back in 1999).
Subjectively, I would rate the 645AFd autofocus speed somewhere in the vicinity of a Nikon N90 (F90 in Europe); and the AFD-II speed somewhere in the range of an N90s (F90x), with similar lighting conditions and maximum apertures.
Put another way, I've shot NASCAR at Dover with the cars coming out of the turn at over 150 MPH onto film with my 645AFd and 300mm f/4.5 telephoto, with no AF issues whatsoever, with conditions in the E.I. 13-14 range (1-2 stops less light than "sunny 16" (E.I. 15) conditions)
The final thing worth mentioning with medium format is the size, wieght and price of the kit. Which is a significant disincentive for many photographers who travel to take photos.
The price issue is easily addressed by one housing manufacturer making a good unit and keeping it in production for several years, since the bodies don't change. Hell, your Hassy housing was in production for over two decades! 
The weight is indeed an issue: Perhaps a much smaller AF rangefinder may be the ticket... I say this as I'm looking at the Fuji GA645 sitting on my desk, wich I take along on for outings when I don't want to drag my camera case along.
All that said. I still have my MF housing. And I do hope one day to stick a digital back on it. I hope that I get to shoot it again.
For me the bottom line is that I do not see any good underwater images being taken with MF in the field. While I don't doubt the sensors are superior - I think the handling of the cameras and the other inherent disadvatages of the system make the final images poorer. But I look forward to seeing some great UW images that encourage me to dust off the ol' hassy in the future.
Alex
Well, take a look at Troy Aitken's work: You can get similar results by just snapping a digiback onto your 503CW! If you have an older body, consider this 503CWD kit instead...
Cheers! 
Dan