Just a thought - and from a non-pilot at that, but from looking at the Google image here
Accident: Lionair B738 at Denpasar on Apr 13th 2013, landed short of runway and came to stop in sea is it possible the crew were victims of an optical illusion? With poor visibility (i.e. a downpour), might it just be possible to mistake the outer edge of the coral reef with the actual coastline further back, at least from a distance? In some photos there are clearly waves breaking at the edge of the reef, and I can imagine that once you've convinced yourself that it is the coastline, it may take time to realise your mistake. I'm not suggesting that this could be the sole cause of the accident, but wonder if it might possibly be a contributing factor?