Because it saves money and our ships aren't being deployed into areas where they need to spend money to protect the ships from anything more than minimal theoretical threats. I could be wrong but I doubt there is a RAN ship deployed anywhere even on exercise, that doesn't have a weapons fit that doesn't outmatch any basic piracy / low level terrorist threat, so to arm them against a higher level threat (ie: another navy) requires investment that isn't necessary. When it is, they get all the good gear you'd expect.
When they do deploy to those areas, they are appropriately armed and equipped. The LHD's which aren't even in-service yet, will be equipped on a permanent basis with 4x 25mm Bushmaster cannons and 6x 12.7mm HMG's.
Those weapons decisively outmatch any non-formal navy threat, so what's the issue? Is someone going to fire anti-ship missiles against us for some reason, outside of any deployment area?
Are you concerned that our Hornet fighters and AP-3C Orions, Wedgetails and Hercules are flying in Malaysia at present without live weapons?