My non-conspiracy theory is that of a similar fate to golfer Payne Stewart’s private jet crash in 1999. They lost cabin pressure and all passed out, but the plane flew for 1500 more miles before crashing in North Dakota.
It was not known why they lost pressure, but it was surmised it was so fast they did not have time to put on 02 masks.
So maybe a small meteor or some space object hit the plane and it was suddenly depressurized but kept flying itself, out of radar range, somewhere in the Pacific, until crashing.
Or, everyone could have been suddenly “Gassed” or “asphyxiated” and the plane kept flying.
The time of useful consciousness at 35,000 feet has been found to be 30 to 60 seconds. Rapid decompression at 35,000 feet MSL could cut that time in half, due to forced exhalation of air from the lungs, but 15 to 30 seconds is still reasonable time to don masks.
Source: http://en.wikipedia.org/wiki/Time_of_useful_consciousness
Your theory does not account for failed transponders (2).