I don't believe the aircraft would have flown any great distance on autopilot with structural damage or a fire on board even with crew incapacitated .
The slow decompression scenario does not make sense either , nobody would ignore the EICAS warning , even if the pilots passed out before that point ( very unlikely) the cabin crew would have noticed masks dropping and after several mins notified cockpit if they did not recognise a descent and in desperation would have carried a portable bottle to the cockpit and energy opened the door.
It really only leaves the options
Deliberate Pilot hi jack
Unknown hi Jackers/s
Or the aircraft was shot down or destroyed in a short space of time...