Two things spring to mind.
ACARS had been disabled BEFORE the final voice transmission. So it seems to me that identification of the voice making the final transmission will greatly assist in steering the investigation towards the person(s) responsible. The hijacking had already commenced.
Secondly reports have suggested the aircraft was climbed to FL450. I can only think of one reason to do this. That would be to increase the cabin altitude. The implications of that should not be lost on anyone.
I can't see how you would know that the ACARS or Transponder had failed.
Retired from the 777 for ten years now so memory not so good.
I haven't flown the triple for a few years either, but I vaguely recall there's an Eicas alert for ACARS? Transponder too I believe?