Thanks all for your replies. I guess perhaps I was also htinking of the other airlines where this happens, it seems to me though that there are big gaps in between check-in and boarding.
For example, as someone pointed out, really transit pax and deaprting pax should not mix, as with arr/dep pax. Anyone going through Perth recently would see the changes being made in the Virgin terminal to get in line with this requirement for no mixing of pax.
As for checking ID at the gate, I have to say that it would be as easy with the QF boarding cards as it would with the DJ barcodes to just give them to someone else. But I have never, ever seen any gate staff pull someone aside for over-the-top hand luggage. And there's been some stuff going through that shouldn't. i guess it's not practical as then would have to be screened and put in the hold which would cause dealys. AGain, down to the check-in staff.
Somehow though the thought of a person checking in at a desk is more comforting to me. Sure, the guys on 9/11 got through, but as pointed out a peron can at least pick up on visual cues like body language. Even if that stops one more incident, isn't that better??
I guess there will never be 100% certainty until ALL baggage and pax are screened and fully sterile lounges are introduced. WHich of course won't happen because the pax and beancounters won't like it.