in my opinion from the little evidence available, it had a depressurisation problem rendering the flight crew and passengers unconscious, resulting in the aircraft flying solely on autopilot and completely unmonitored from the malacca straights on an approximate track taking it over the indian ocean towards the island of madagascar via diago garcia, where at some point it ran out fuel.
Very unlikely. If the cabin altitude went to even 10,000', there would be a loud aural alert in the cockpit plus an EICAS message telling the flight crew that there was a pressurisation problem. I'm sure the pilots are regularly checked for health and wouldn't find 10,000' much of a problem. If they did succumb to lack of oxygen without realising there was anything wrong with pressurisation, the autopilot would have taken them to their destination and beyond (at their current cruise altitude). Also, as previously stated, depressurisation shouldn't have affected their transponders.