There is no contracted DOF. Nothing about the lens changes. It is still a 105mm lens and works the same way. As far as DOF, it does not change. We often talk in terms of 35mm equivalents, because that is what we are used to. But it is the length of the lens and aperture that control the DOF.
Lens lengths in terms of 35mm equivalents
35mm film language: 105mm = 105mm
6x4.5 MF language (larger film size): 105mm = 80mm
D100 (smaller CCD): 105mm = 160mm
4"x5" view camera: 105mm = 35mm
The inherent DOF based on focal length is one reason MF underwater hasn't been all that popular and one reason consumer digicams are so well received. The really small CCDs on consumer digicams provide incredible depth of field vis-a-vie their 35mm counterparts at the same 35mm focal length equivalent. If you wanted to hypothetically shoot a 645 MF camera underwater with a lens, say equivalent to the 60mm Micro, you would need a 100mm MF lens. You would get the same angle of view, but the DOF would be reduced (at equivalent f/stop) because it is still a 100mm lens vs. a 60mm.
There is no doubt that the 60mm is a more versatile lens than the 105mm, without the crop factor and even more so with the crop factor. That is because most shooters and shots are not 1:1. Even small fishies (say 1.5" long) rarely fill the entire frame. They often don't let you get that close. I've shot entire fish, even octopus with the 105mm (on film camera) with the 105mm. Obviously, it would get far more difficult with the 1.5 crop factor.
I've shot the 200mm macro lens. This reduces DOF to 1/4 of the 105mm. With the 200mm I found that I often had to back up to get 1:1, but still had plenty of light thanks to two SS-200 strobes. Shooting whole normal size fishes was impossible, too far away. Not very versatile.
As far as AF vs. MF, true macro shooters will tell you MF is the way to go. But, gulp, I just can't do it underwater and not very well topside either. The AF does better than my eyes. I was told that the only way to shoot the 200mm with its reduced DOF was manual focus. The lens and port were so long and heavy I couldn't accurately turn the focus control knob at the end of the port and hold the thing steady, so I shot AF. It was frustrating as it was hard to get a focus lock and every movement of me or the subject required a refocus, but it was less frustrating than trying to manually focus. The proper technique is to set the focus manually and move yourself until the subject is in focus. Again, I found my judgement of when the subject was in focus not very good compared to the camera. So, I'm with you on AF.
I intend to shoot the 105mm with the D100 (=160mm) knowing full well I'll sacrifice versatility to shoot larger subjects, but the extra working distance for a 1:1 will be a blessing for true macro work and I know the strobes can support it. They produced plenty of light for macro work with the 105mm and 2x teleconverter (2 stop loss of light) at f/22.
