A comment on disabling avionics:
In the scenario of a flight deck invasion, why would a perpetrator bent on plunging an aircraft into the sea care about transponders/acars/radio? There's nothing that any ground agency could do about it, nor would disabling change the facts nor would it hide the act. So why? Who would benefit?
It would be astonishing if the passport thing turns out to be a red herring. With regard to the number of passengers flying under false pretenses: what happened in the innocent 80's is hardly a template for what should be common today, especially post-9/11.