1. If they blew the cockpit door off that resulted in cabin decompression that eventually lead to a dead crew and passangers, then the hijackers would have been seriously pre-occupied and likely didn’t have time to turn all the transponders off.
2. The search planes should be equipped with a dummy Cell Phone tower equipment and go around looking for roaming cells.
3. Is it at all possible that the actual black boxes on the plane were disabled prior to takeoff?
No. The radar transponder would have to squawk the assigned code or ATC would have known immediately the transponder was not reporting.
The other "black boxes" you refer to on this plane, do a myriad of things but most are passive collectors of data except the ELT.
The ELT would only be activated by crash or contact with water but not transmit in normal flight.
Or maybe they "use enough dynamite there Butch?" and took the complete nose off the aircraft. And unlike Flight 800, it flew straight and level for hours.