Possibly a bomb went off on board. Terrorists plan their actions meticulously even to the point where the plane will go down. If they don't want it found right away they will chose a spot where the water is deep. The reason they don't want it found? Because it probably was a dry run for other targets and they found a new method to conceal the explosive and were trying it out. My sympathy to all the victims of this terrible tragedy.
Yes, it is a crime to use stolen passports, but there are many crimes that fall well short of terrorism.
All we know for certain is that two individuals boarded a flight using documentation that was not theirs. And that is all we know.
I flew Malaysian Airlines from Singapore to The Maldives with a 2 hour layover in Kuala Lumpur in January. I don't remember them running my passport through any kind of a computer check. If I remember right, it was only a visual check.