JT,
According to Flightglobal's Special Safety Bulletin regarding this accident,
the co-pilot was in control of the landing. The aircraft hit a pocket of heavy rain at a fairly low altitude (flaps and slats out for the landing) and lost sight of the runway, at which point the Captain took over the landing. The Captain then elected a TOGA missed approach but the aircraft did not respond to the climb quick enough or as expected and settled into the water. If true, it might suggest that heavy rain does indeed affect lift capability of the wings with slats and flaps out at slow speeds.
TD