I believe that though the submarines were changed dramatically with Finding Nemo, it was still considered an existing attraction and did not need to be retrofitted to comply with ADA. Disney DID make an alternate viewing experience (IMO probably for goodwill/fair treatment but possibly under lawyers' advice, I suppose). But I would consider the Nemo overlay similar in scope to the Tom Sawyer's Island overlay--a lot of the decor has changed but the basic infrastructure remains from the past.
Also, the wilderness play area in DCA was built well after ADA and there are a lot of areas/activities that aren't wheelchair accessible either (I had some trouble with the literal rope bridges myself, and I don't use any wheels!). So even if they built Tom Sawyer's Island brand new, I would imagine there would still be quite a few areas that would not be suitable for a wheelchair, though the trails themselves would probably be easier to navigate.