My hypotheses:
One or both pilots were in on it. This is because of the sophistication of what was done to turn off electronic communications equipment and how the plane was flown after its transponder was turned off, which shows airline-pilot-level familiarity with the systems, radar zones in that specific region, etc. and intent other than just suicide.
All passengers and the rest of the crew might have been killed by flying the plane for a while at 40,000 ft. while depressurized. Oxygen masks for passengers might not have a large duration of oxygen or be able to keep someone alive for a prolonged period at 40k. If they weren't killed, they'll be on the plane for the horrible purpose below or as a backup if the plane is discovered, as hostages.
The jet had enough fuel to make it to its intended landing area. The folks who pulled this off obviously planned things out. Figuring out if the plane has enough fuel is one of the easier parts of the plan.
The landing area is China or Pakistan -- probably western China (as otherwise, it would need to overfly all of India and then have just barely enough range to land in Pakistan).
The jet is intended to be used in a terrorist activity, but against whom? If it were to be crashed into some Chinese buildings, why hijack it instead of doing it while inbound? Maybe they couldn't get pilots who were willing to do that but who were willing to hijack it? It would be hard to move the airliner all across the world to go crash it into something in the US. Is Russia the target? They are another country that gets attacked by Muslims. Is Israel the target? Do they think that they can refit the plane and sneak it in there or force Israel to shoot down an airliner with a bunch of people on it (or bodies)?
My hope is that the passengers are still alive and get found before any next steps are done by the terrorists.