All those things COULD move to smartphone apps. But its unlikely that they will anytime soon, especially when there are so few phones that support NFC (and support the right flavors of NFC in the right way)
Even if EFTPOS (and the entities that own it) brought in a way to pay for EFTPOS transactions via a NFC phone, there would still be tens of thousands of businesses out there that don't support such payments. And the 1000s of ATMs would need to be updated too (although at least one bank has a system where you dont need a card, you just log into your smartphone online banking app and it gives you a token you input into the ATM and both systems talk to each other and give you money)
As for the Go Card, how many of the NFC-enabled phones out there are capable of supporting the proprietary MIFARE Classic format that the cards use? Not to mention issues it could cause
And for the health cards, same thing as the EFTPOS, how long will it take for all those doctors, hospitals, pharmacies, optometrists, dentists, physios and other medicos to update their gear to support it? Not that the government would want to spend the costs involved in making a medicare card app...