First, since the D100 is no longer being made by Nikon, it will die a slow death and housings will probably parallel the process. You probably still have some time to get a D100 set-up, but it looks like the D70 will be the Nikon way to go for awhile.
To the point of TTL, I have some prodding to belie on James and others using digi TTL. Since I have only shot manual since converting to a D100, I haven't had any of this experience underwater, but when you are shooting the Fuji S2, what does your histogram look like after a ttl exposure? Is it still shy of the highlights, forcing you to use post processing tools like PS CS? Or is the exposure perfect and no post processing is required other than sizing, sharpening etc?
If you still have to post process colors, TTL IMHO is as good as manual and vice versa. In manual mode, you should expose your imaged to where the histogram is not hitting the right side of the X axis. This means that you are underexposed, and the post processing of the your image can be brought into a good dynamic range with Photoshop. It's the same with TTL. If you are having to post process color adjustments, especially to bring the image to the right exposure when using TTL, what's the difference? And with a 1.5 to 2 f-stop flexibility in digital images (shooting Adobe II) you can "bring in" underexposed images to make them nicely exposed.
The advantage I see using TTL is that one shot wonders are more likely to come out with TTL than with manual, since guessing is so, well, a guestimate. TTL will probably get you close and with a 1.5-2 f-stop forgiveness in digital, you will likely get a good exposure.
Joe