edit: 5D housings might be cheaper but on the other hand 5D body won't stay the same over future generations as the 1D bodies usually do ... but your 1Ds Ewa-Bag might be compatible to the 5D too
The other thing to remember is time. I think that it will be unlikely that the will be a 5D housing out until this time next year. Whereas you can buy a 1D/1DS housing today. You can take a lot of pictures in one year!
I also think that the housing manufacturers will not be queuing up to make housing for this camera. Ikelite, who is normally one of the fastest, tend to focus on mass market cameras. I can see Subal and Sea & Sea supporting this camera. Maybe Sealux too. Not convinced about Seacam, maybe?
The 5D is expensive and likely to generate low numbers of sales for UW shooting. The clincher would be if it was full frame. If it is, then fisheye factor will make this a popular choice for UW photography and may persuade several companies to go with it.
Judging from the interest expressed for my filters I would say that Nikon D70 + D100 out number Canon DSLRs about 3-4:1 in digital underwater photography.
So an expensive, but sub-pro Canon, is unlikely to be a great investment for housing makers.
I think that the 1DS Mk2 replacement will not have the same body. The main criticism of that camera by land photographers is the ergonomics of the body. SO I think that the current camera is the last that will fit in that housing (apart from the 1D Mk2N).