We are Australians and will flying from Singapore to Shanghai with a 3 hour transit in Hong Kong

In case that your real itinerary, including layovers and similar is Singapore - Hong Kong - Shanghai - South Korea, you are definitely qualified for 144 hours visa free transit. You have mentioned that your cruise will visit South Korea, Hong Kong and some other destinations... Here one vital detail. It is definitely OK if your first port call immediately after you depart from Shanghai is in South Korea, but it cannot be in mainland China or in Hong Kong! Anyway, it is entirely fine that your cruise visit Hong Kong later, but not immediately after Shanghai. So, just check precisely what is your first port call immediately after Shanghai and if it is some port in South Korea or Japan or Taiwan, you are qualified for 144 hours visa free transit.

Further to this we fly Brisbane to Singapore. Stay the night then next day fly to Shanghai via Hong Kong.

In case that your itinerary is precisely and without any other omitted place, Brisbane - Singapore - Hong Kong - Shanghai - South Korea, then you are definitely eligible for 144 hours visa free transit in Shanghai. Now, here we have to clear one detail... Your cruise should not have any mainland Chinese or Hong Kong port call immediately after you leave Shanghai. It is perfectly fine to visit Hong Kong, but just after you have had some port or more of them in South Korea and/or Japan for example. Plainly speaking, your cruise cannot have an itinerary Shanghai - Hong Kong - Busan, but it is definitely fine if it is Shanghai - Busan - Hong Kong - etc.... Basically, all you should do is to look at the itinerary of your cruise and if your first port call after Shanghai is not in mainland China or Hong Kong, you will enjoy 144 hours visa free transit. You should bring your documents in hard copy.