There has been and always will be a backlog of work at Co-Dock. Its big, it can support almost any type of operation. Its convenient. Just the big ships (defence) and big commercial (manly ferries, cruise stuff) mean its schedule isn't flexible.
Ships aren't getting smaller, but bigger. Cairncross may exist in that future, but it has langished for over 2 decades now, and has all the problems of a brownfields site, and a greenfields site. It is not really located in an industrial area anymore and planning to make it a residential area means its possible conversion even as a civilian ship yard is probably marginal. IMO you would have more luck and success with Cockatoo Island.
IMO subs Newcastle and Kembla seem to be more obvious, and there seems to be a fair bit of support for Kembla (with easier deep water and industry support). Sydney has all the nuclear know how. That's how its ended up, no one else built any nuclear facilities, no one else has any academic or research in that space nationally. We have had multiple nuclear reactors running in Sydney for over 60 years across 3 series/generations of reactors. If any other state wants in, they can build a civilian nuclear reactors, university and tafe/trade programs, waste storage, secure fuel import and waste export travel paths, and try. I'm not sure on what grounds something else other than Kembla/Newcastle would get serious consideration. ANSTO is what it is, a national nuclear facility. There is no other national nuclear facility. There isn't anything like it in the whole southern hemisphere (inc Brazil and Argentina who have sizable national nuclear centres).
Somethings can be moved, some things cannot.
The only other consideration is really that the American are going to base stuff over at WA. But that is different, and interconnected. We will build them down in S.A (mostly installing prebuilt modules from elsewhere), but again, different. SA may be the site of a nuclear fuel/reactor assembly centre, but that is still decades away. Nuclear tech is hard for the US/UK/France/Russia/China, they don't just randomly move around their key sites and create greenfield problems. Los Alamos is still Los Alamos.
Being further away is a good thing, it makes it that much harder for drones/diesels to follow.