Too late for the original poster, but I live on Hong Kong side and plan on being at the Hong Kong Station check-in counters -- not the airport -- about 2 hours before my flight.
There is, in my experience, rarely a line at the NWA counter, and the train takes 24 minutes to get to the station. I check in at 6:30, arrive at the airport by 7:15 or earlier (depending how long I had to wait for a train), and still have to kill time before boarding. This was true even before I had my Hong Kong ID and had to queue up in the visitors' line at immigration.
So it's still early, but I don't think you need to plan to be at the *airport* two hours in advance.