I think soft spots are most likely caused by some kind of impact. Something needs to separate the laminate from the foam core. Another cause could be water seeping in through a crack in the gel coat and eating away at the laminate. I'm not sure what causes soft decks, but I would guess it would be standing on or otherwise point-loading the deck, causing it to bow inwards and separating the laminate from the foam core. Another cause might be air in the hulls heating up and expanding, causing the hulls to bulge out.
As for prevention, I would say fix cracks in the gel coat as soon as you find them, make sure you keep the insides of your hulls dry, and leave drain plugs out on the beach to let the pressure equalize.
This is just me thinking outloud, so I might be totally off. Anyone else help me out here?
Narragansett Bay, RI