Certain fish and corals that are easily bred will never have a shortage. If the price of wild caught clownfish goes up, the demand for aquacultured clownfish will increase, leveling itself out.
As far as species that cannot be bred at this time, it's hard to say. The number of saltwater hobbyists is definitely increasing, so the demand is increasing. I'm sure there will be a shortage of certain species.
However, it seems that as more is being learned about the hobby, and better equipment keeps coming out, the possibility to breed some of these other species might be right around the corner. It would be great if we could aquaculture most fish, and not have to worry about a shortage in the oceans reefs.