Any any stray shot by some trigger-happy gun nut would likely pierce the fuselage and start decompressurization, ala Goldfinger.
No, it wouldn't. Repeated tests have shown this will not happen. If you think a hole the width of a pencil will cause a plane to lose pressure that quickly, you might want to check your physics book again.
Also, terrorist holds lady with knife to neck and tells you put down your weapon (while unseen terrorist sneaks up behind you with box-cutter).
So on a crowded plane, there would be no one behind you to see this second terrorist sneak up behind you? Even if they hold a knife to someone's neck, you're still defeating their purpose of taking over the plane. The pilot now has time to radio an emergency and make a rapid descent or throw the plane into violent maneuvers to upset their balance.
I like this, too, but what's to stop the bad guys from faking the secret frequency and crashing the plane from the safety of their hideout?
And people say I have an active imagination. How do you propose the bad guys fake this signal from a cave in Pakistan to a plane flying over the Alps? Or over the Indian Ocean? You do realize the power required to send this signal, the technology to continually track the plane in flight and the equipment needed to do all this isn't something you can go to your local Radio. . . er, Best Buy and pick up on a whim.
Stop over thinking this. Today, if someone tries to hijack a plane from within the passenger compartment, they will fail. They might be able to kill a few people on board, but they will most likely die in the process and so will not accomplish their mission.