Heres something different to consider. How many times has a disaster been caused by a series of small unrelated errors and or malfunctions?
Consider a scenario similar to that of the Payne Stewart mishap.
A slow loss of cabin pressure due to an electrical fault of ruptured bellows, and a malfunction of the environmental warning, would cause the pax and crew to simply fall asleep. This would explain the loss of communication. In addition, maintenance in this part of the world is not exactly the best. Its common to have warning circuits disabled if a redundant system is still working, or the system in not considered vital to flight.
With the auto pilot on, the plane would continue on its course until it ran out of fuel, unless a slumping or partially incapacitated crew member applied enough pressure to the control yoke to override the auto pilot, and put the plane in a gentle descent. This would explain the loss of altitude and course deviation, if a deviation took place at all. The VCAF contends that they tracked the aircraft on a westerly course.
The plane gently bellies in on smooth shallow water, remaining intact, and sinks to the bottom. Since an airliner has a pressure hull, it could withstand submergence as the malfunctioning outflow valves allow the cabin to flood. Since we gain 1 atmosphere every 60 feet, the pressure hull could easily withstand 2 atmospheres of pressure so long as incoming water continues to compress the trapped air. This would explain why there is no or little debris to locate. It may also explain why some cell phones appear to be working.
Aircraft landing intact under autopilot control is not as unusual as one might think. While in the USAF, I was required to read all aircraft mishap reports. During my tenure, there was about a dozen instances where aircraft belly landed in the desert under autopilot, then repaired and returned to service. In some instances the aircraft landed without a pilot. In one case, the aircraft was located with the engine running at idle. Apparently the pilot just wanted to take a ride in the ejection seat. Ooops!