I know it's way too early to be speculating what happened, but if the aircraft is reasonably well intact on the bottom of the sea floor, then an inflight break-up due to weather is most unlikely.
However, the possibility of a double engine flameout due to heavy and intense rain from TS cells in the area at the time, can not be ruled out, as a possible cause.
Such an occurrence has happened before in Indonesian airspace to a Garuda 737-300 flight from Lombok to Jogjakarta which suffered a double engine flameout after passing Surabaya flying in intense thunderstorm conditions. The crew glided the aircraft down from cruising level, whilst trying to relight the engines, but were unsuccessful and they ended up ditching the aircraft in the Solo river. Surprisingly, all aboard survived, except one flight attendant who slipped and fell during the emergency evacuation and later drowned.
This incident was discussed on PPrune some years ago here, for those interested.
http://www.pprune.org/questions/2203...g-details.html