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You're assuming that the passengers are still alive (the plane climbed to 45,000 feet after disabling its transponder), and if they are, that they haven't been intimidated into giving up their phones.

What does getting the last known cell phone tower contact have anything to do with whether anyone is alive? Like the OP says, all that is a single phone making contact with the nearest tower.

Most people still turn their phones off before a flight to save power or because they think it will keep them safe. If they are dead, they can't turn the phones back on and the hijackers can go around searching for phones if they really want to. So it's pretty unlikely that phones will attempt to make contact with cell towers.

But assuming that a phone does make contact, there would be massive cooperation required to detect it. The airline and victims' families would have to give a list of phone numbers that could be on the flight, and all the carriers in the region would search through their towers' logs to see if any of those IMEIs (assuming they keep those logs for at least a week).

All it takes is one phone to be on, regardless of human intervention. I would wager someone forgot to turn their phone off. Nevertheless, if the flight was hijacked and the hijackers were pros, as they clearly must be, they might have had a cell jammer. Regarding IMEIs, cell numbers of passengers, and tower logs, well that's what we have all those 3 letter acronym agencies for. I'm sure they haven't just been sitting around all this time. I don't think it's just the navy and air force sending search and rescue.

These guys were also incredibly prepared it seems. I would suggest that it would be unlikely that passengers, if they were still alive, would be allowed to just move about and grab things. They could be blindfolded and told not to move, for example, during landing, refueling, and so forth (though blindfolds may not be as relevant at night.

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