I was thinking of this possibility yesterday. But it doesn’t seem reasonable because in today’s post-9/11 world, any plane flying without a transponder will be shot down. The terrorists have to know this.
No, that's not going to happen outside a war zone. There are too many benign causes for a transponder malfunction.
A plane without a transponder will be investigated. But, it won't be shot down unless there is an unambiguous indication of a threat.
I wonder why pilots even have the ability to shut off the transponder in the first place.