i agree with archman. there is plenty of literature on the effects of hurricanes on reef systems. the reef isn't just damaged structurally by the high energy waves that pound it, it's also damaged biologically because of the sudden drop in salinity levels (among other factors).
the remarkable thing about reefs is that having been around for centuries, they can recover from such large scale damage as hurricanes and typhoons. if they've been able to persist is those areas that are periodically struck and damaged, chances are, they're adapted to that kind of stress. (e.g. more massive corals in high surge areas).
almost analogous to forest fires, with our concerns over loss of biodiversity, etc. but eventually we learned that it's part of the natural cycle of the forests.
however, if you add more negative stresses (e.g. overfishing, disease, bleaching... the list is long...) you're sort of weakening the ability of the reef to recover. and there's where the danger (and the challenge for us) lies. it truly is a heavy blow to see a reef so heavily damaged, especially since we have precious few pristine reefs left.
