Unless ADF/RAN doctrine on deployment of the LHD differs from other that of other RAN vessels, then yes, three LHD's really should have been ordered. With only two having been ordered, most of the time one will be either on a deployment or available for deployment, with a surge capacity of up to two LHD's being available.
Where this can break down is when one of the LHD's is undergoing a refit, ship trials and workups, etc anything that can make vessel unavailable for deployment for significant periods of time. This leaves the other LHD as the one to be either available for a deployment, or more importantly might already be on a deployment. It is that last bit where the wheels start to come off and things break down.
Unless the doctrine is for one LHD to be kept in/near Australia for deployment while the other is undergoing refit, then the RAN could one that one of the LHD's might be deployed away from Australia on a HADR mission, or serving as a command or mothership for anti-piracy ops like off the coast of Africa, on a show the flag mission, participating in international exercises, etc. There are quite a number of different potential situations where with only two LHD's, something could occur that Australia would want or feel the need to respond, but be unable to because there was no LHD available to respond with in the needed timeframe.
Also as has been pointed out regarding the deployments of Bill & Ben... only having two assets, especially such useful that can support operating helicopters, have a hospital, have command/comms facilities, those assets are likely to be worked often, and hard. As has been observed, this causes problems balancing the operational desires and needs of the ADF, with the vessel's need for maintenance and periodic refit. Having a third vessel can spread the workload around a bit more, allowing more time for a vessel to be alongside or in drydock.
-Cheers