Most pet shops buy their marine fish from wholesalers. The source of wild caught fish is seldom known for certain. Captive bred fish are becoming more common, but the number of species is very limited. Clownfish, seahorses, perhaps a few others, are all that are available in quantity. Captive bred fish are always more expensive, though ultimately worth the price. Nevertheless, most people go for the lower price. Inexperienced aquarists may see a Percula clown at one shop for $6.00, and at another place for $20.00. The more expensive is captive bred and far more hardy, but this distinction may not be as important as price.
The issue is far more global and broader than the ornamental fish industry. Rainforests are disappearing in South America and Asia, along with most of the natural world, including the reefs. Uncontrolled human population growth and associated extreme poverty cause poor nations to sell whatever they have. Immediate survival needs take precedence over any other consideration.
The world's reefs are being destroyed by human expansion and pollution. Fish collecting is insignificant in comparison to the siltation and water quality degradation from expanding human activity. Look at the waters around Miami, and even the Keys.
The use of cyanide reflects poverty. Cyanide is cheap, and lots of fish can be easily collected. Some collecting stations claim to use only nets, but a lot of deception goes on in impoverished areas. I know this from first hand observation.
If you want to save the reefs, support programs that help to bring about a more eqitable distribution of wealth. This runs contrary to most American business interests and (therefore) US government policy. Also support any programs that provides birth control assistance and any other population control measures around the world, including here in the U.S. There are far too many people on this planet. The Earth belongs to other creatures as much as it belongs to us, and we have shamelessly dispossessed whole species and annihilated entitire ecosystems simply because we are unwilling to limit our numbers, or because we want to build a resort or an industrial plant.
China's 1.3 billion people have managed to almost wipe out much of SE Asia's wildlife, simply by the power of their ability to pay for and consume enormous quantities of animals and fish, for food and as traditionl medicine. That, by the way, is where all the seahorses have disappeared to, along with countless other vulnerable populations of animals. This is only one example. We are all at least equally responsible.
As Pogo observed, "we have met the enemy, and it is us". I don't think the fish importation industry is a major issue, though I agree it should be more carefully regulated, and captive breeding expanded. This means all of us have to be willing to pay a lot more for our fish and inverts. If nothing else, the aquarium hobby raises awareness and creates vocal partisans for the protection of sealife.