Purely speculating here - could lightning have caused an electrical short circuit, which for whatever reason have caused a catastrophic explosion? For instance, didn't a short circuit in the fuel tank bring down TWA 800? I mean, some things just don't add up here...
It would need to be one heckava bolt to knock out the entire aircraft! The 330 is build with several redundant systems to prevent this from occuring. However a direct strike to the cockpit would probably set things in motion.
Remember they didn't launch a search until the next checkpoint was missed over the Cape Verde Islands, several hours past Brasil's last checkpoint. Both the ELT and boxes should be pinging and we haven't heard any chatter from pilots over the route. If our satellites can find junk autos in Iowa cornfields from 800 miles in space, they can certainly find an ELT.