Personally I would book the direct A380 flight on EK406 rather than either EK404 or EK408 which has a stopover enroute and less comfortable J product.
Otherwise depending on where you are connecting from, I would book the later one which arrives in to Melbourne in the morning. I would not worry so much about how busy the lounge might be, but be more concerned about the departure and arrival times at origin and destination, and stopover time.