Recheck you flight times. It was only 50 minutes after takeoff before the problem occurred. Not unusual for and exploding tire and damaged components to take that long to manifest itself.
True, things can smolder for quite awhile undetected until its too late.
Another pilot (link I posted earlier on this thread) speculated it was the likely the nosewheel gear/tire that smoldered and finally either caught fire or filled the cabin with smoke.
Speculation then went to the pilot changing course as the radar and records show, BUT the course correction was to the closest airport Palau Langkawi a 13,000 foot strip with an approach over water at night with no obstacles. He did not turn back to Kuala Lampur because he knew he had 8,000 foot ridges to cross. He knew the terrain was friendlier towards Langkawi and also a shorter distance. Before they could make it to Palau Langkawi the pilot, co-pilot and perhaps passengers as well were overcome by the smoke and went unconscious. Plane kept flying on the course set until it ran out of fuel and crashed in the Indian Ocean, some seven hours later.
Whether or not that's what actually happen we may never know, but that's one of the two or three reasonable explanations I've read.
In some ways, it's reminiscent of the Payne Stewart tragedy years ago.