I think that I agree with Don. It sounds like you basically have a hole in your floor. Does it extend out to the edge of the floor or is it basically just a hole more in the middle of the floor? It should be fairly easy to just cut the rest of the bad wood out and cut a new piece of plywood to fit the hole. Depending on exactly where it is you would likely just have to add some plywood strips under the edges of the patch that you can glue and screw to both sides of the joints. I suggest about 3" on each side of the joints for your plywood splice pieces. Use a good grade of waterproof wood glue and some decking screws. This type of joint is pretty much as strong as the original plywood. This is also how AS recommended repairing the floor in my 1973 shop manual.
If you decide that you want to use some sort of overlay on top of your subfloor to give you a better base for flooring then you might want to consider 1/4" underlayment plywood. It would be a lot lighter than the hardi board and could be made more waterproof with some type of paint or sealer if you want. Also your choice of flooring could help with the waterproofing.
It is also possible, by the way, to get Polyboard in 1/4" thickness. I don't know if you have read any of the threads about my use of Polyboard to replace my subflooring but it is a totaly waterproof material that is a lot more flexible than Hardi board would be. It would make a fantastic floor underlayment. I just checked pricing today and 1/4" Polyboard at my local supplier goes for $41.35 per 4 x 8 sheet. Polyboard prices have gone up since I bought mine by the way. If you are interested in checking out the Polyboard take a look at the following thread:
I believe I included information there about where to get it.