I think the big point, lowerlobe, is to ask "what are they trying to achieve?"
To put a pilot through the wringer to "prevent him potentially gaining access to the flight deck" is possibly one of the most stupid and misdirected security excuses I've ever heard. And I've had exactly that statement thrown at me going through Brisbane.
Now if they said said "we're going to run a quick computer check on your ASIC" I would say "Bravo! Focused security aimed where it is needed!"
Alas it will never happen. The problem we have is misdirected, unguided, unfocused security so Joe Public gets the "feelgood" factor. "The two pilots have been checked for weapons. That's good. I'll be safe on this flight."
I have an idea for a Monty Python-like sketch: A guy in white robe, Bin Laden style beard, and islamic cap wearing pilot wings and ASIC goes through security. They pull him up, explosive test him, confiscate a tube of toothpaste, check his carry-on bag, umbrella - nothing else is found. Then the security guy goes: "Right, off you go then! Fly safely sir!"