If a pilot thinks he needs explosives to crash a plane, he may be overlooking something.

You just need to ID him, not search him. Check his badge, call it in if you're not sure, done.

Congratulations. You've just introduced a single point of failure to the system: anyone with a badge forged well enough to fool a security guard now has carte blanche.

Not really - make all pilots have their badge authenticated at the security point with a computer fetching the image from a database and comparing it with:

1) the pilot 2) the picture of the id

Done.

Anyone who boards a plane as a pilot, or co-pilot, has pretty much charte blanche.