SpannerInTheWerks -
You might not be able to "imagine anyone knowingly flying directly into a known area of bad weather?".....but the fact is, it has happened before on too many occasions. As to the Captain taking his break at the time, I find THAT hard to believe if he knew they were going to be in an area of storms. Unless, that is, he told the relief crew to avoid those areas and they didn't for some reason.
About all we can do is speculate unfortunately, because the chances of recovering any meaningful data does not look good at this point.
Speculation-wise, I'd say that weather was a factor as was computerized flight controls.