It's way to early to know if it was a structural failure that led to depressurization, or a hijacking that led to crew incapacitation, or smoke in the cockpit that led to incapacitation, or even to know if they were conscious at impact.
But it's important to know that at 38,000 feet, in the event of a rapid depressurization, the time to get the oxygen mask on is very short before you become incapacitated. Meaning seconds.
It's not like holding your breath. The air in your lungs instantly thins out to the ambient pressure -- you can't hold it in. If you don't get the oxygen mask on and breathe 100 percent oxygen within a few seconds, you probably will pass out, or at least won't have the coordination and ability to think enough to accomplish the donning of the mask, then you will pass out.
That's why, per FAA rules (U.S.) above 25,000 feet if one of the pilots leaves his station in the cockpit then the other pilot must put on his oxygen mask. It helps assure someone will remain conscious in the event of a rapid depressurization.
Just a hunch but the steady altitude loss described by all the sources of information for this accident, and the fact that they didn't appear to take action to avoid the terrain as they descended, and the fact that there was no distress call, strongly suggest incapacitation of the crew.
Why they might have been incapacitated is open to a wide range of possibilities.
