Agreed. Running luggage and boarders past explosive detection machines is probably worthwhile, and not much of an affront to customer dignity. Whether the passenger or luggage owner is identified accurately is largely irrelevant for this.
Expect most aircraft-targeted terrorism in the future to originate outside the aircraft. Weapons will probably be small ground launched missles or machine guns.
Yep. Hijacking is now extremely difficult, bordering on impossible, due to (in order of importance) the new "fight back at all costs" mentality, reinforced cockpit doors, and (at least somewhat) enhanced checkpoint security. The threat of explosives in checked luggage is essentially gone, since checked bags are now universally screened for this, greatly reducing the probability of a successful attack and increasing the likelihood of getting caught. The threat of a bomb in a carry-on has been reduced, and this shrinking weakness will be gone before long.
That leaves attacks from outside the aircraft as the most significant threat. On the negative side, there are no real defenses against such an attack in place. Perimeter security is not good, and is very difficult (nearly impossible) and prohibitively expensive to improve substantially. Aircraft do not yet have defensive measures, and changing that will take money (not to mention a decision to do so). On the positive side, shoulder-fired missiles do not have a high success rate in bringing down airliners. Attacks have happened (mostly in Africa), and they sometimes bring down the plane, but more frequently the plane lands safely, albeit with one pissed-off pilot and a bunch of passengers who need to change their pants.