Seems unlikely to have a birdstrike shut off the transponder.
But we're having to think of every possibility.

I saw a report of an AD on the 777 describing corrosion around an antenna mounting that might lead to decompression.
Then got to thinking that if the transponder antenna mount were torn away the lack of antenna would look like loss of transponder to the ground stations.

Combine with sloppy flight deck behavior such that no pilot could get to his mask in time then you have the Payne Stewart scenario of a plane flying on autopilot with no live souls on board until it runs out of fuel.

But you'd expect one of the countries along the route to pick up the ghost plane on radar - so this theory has holes in it.

I think the high-probability one is hijacking followed by unauthorized pilot flying toward some target (like the high towers in Kuala Lumpur?) with a 911 type crash in mind.
But since this flight went out over water at night, perhaps they inadvertently descended into the water while still trying to figure out how to aim for their target?