"There is an emergency code for access to the flight deck in case of both pilot incapacitation."
Yes, but if someone has gained control of the flight deck and knows what switch to toggle, that access is denied. It is just one position.
Looking around the internet tonight there are some fascinating, wild theories that sadly the longer the time to find the aircraft is, the slightly more believable they could be. The trouble is nowadays with governments, one doesn't always know what to believe and even stopped clocks can be right at times.
At the moment one shouldn't assume official intervention is the reason for delay when incompetence or just plain bad luck is the reason. Although as TWA800 and elements surrounding September 11 show, many people articulate reasoned counterpoints to the officially stated narratives. The real reasons? Way out of my league and knowledge just like most posters here.