It could be any number of things. In most cases its collection difficulty, usually depth. Take the peppermint dwarf angel. I don't suppose we really know for sure, but it doesn't appear to be rare necessarily, just really hard to collect with a poor survival rate thus making it very scarce in the hobby.
Fish usually are rare because of collection issues (depth and usually die when brought to the surface), because they get too stressed with shipment and usually die, or perhaps most commonly because they are only native to a region that does not allow, or greatly limits, fish capture. There are many clowns that we do not see in the hobby simply because of where they live and laws protecting them etc.
Aquarium Reef fishes are expensive because they are hard to catch.Most of them hide in the rocks ,nets cant be used because they will get breaked by the reef. Poison is what is used mostly to catch the aquarium fish from the reefs.Dont belive the phrase,,hand caught without poison,, its a fairy tale.That looks like a 5000$ fish if somebody is ready to pay.Gramma dejongi ,a soird of gramma loreto is cloose to 3000 $ and its not a spectacular fish eyther.Its better to buy aquacultured fist instead of the wild ones so the wild reefs arent poluted with tons of poison just to catch a few small aquarium fish.