What I've read elsewhere (whether true or not) is that Finding Nemo Subs is likely safe for a while...after that investment, it doesn't make sense to just take them out after 5 years. And I understand that a fair portion of the Autopia track goes over the subs building, so it would be difficult to replace one ride without the other. Not impossible, but I'd personally be rather surprised if anything that drastic happened in the next 5 years, at a minimum.
It seems plausible to me that they might shorten Autopia at some point in the not-so-distant future, though. Operating/maintenance costs could go down a bit and it could free up some space (probably the parts of the track that used to be in Fantasyland's old Autopia, granted).