Well, if we do find this aircraft in the Indian ocean, that really only leaves one of two most likely scenarios:
1. Hi-jack
2. Foul play amongst one of the crew members. All it would take would be one crew member goes to the bathroom and the guy on the flight deck locks him out.
Hypoxia is still a possibility, but less so than 1 and 2 above. One needs a really big hole to get a decompression, and that would have been followed by a rapid descent, which didn't happen here. And we know the pressurization was functioning correctly since they cruised for awhile, so you can reasonably rule out a improperly set pressurization control
Mmm not true at all. One only needs a hole bigger than the outflow valves diameter and they are not usually that big. The alternative would be loss of pressurisation due to loss of incoming air from the ac packs 1&2 (can any 777 drivers confirm if they fail closed with power loss?) which could have conceivably happened when/if everything else failed rendering comms and txponder in-op.