For us it costs about $10 for a 3 incher.
I can break down the costs roughly but take my words with a grain of salt .
Anyway, suppose it costs them $5 to get one clown loach. That $5 was made because the fisherman had to be paid, the transporters had to be paid, deaths had to be accounted for, food had to be fed, a few various other figures that all come into play before live aquaria gets them. Now, Live aquaria has them. They will quarantine them, continue to care for them, and possibly have some of them die before they are ready to be sold. Now, the quarantining means that they must be fed and housed for a longer period of time thus taking up space other fish could have been using so they raise the price to make up some of the money that they could have made by not bothering to quarantine the fish. Since they are "Live Aquaria", they are a well known brand to fish keepers. They are the rolex to the fish world, easily recognizable and trusted to be of high quality. They raise the price because of their good brand.
Over all I'd reckon that the main factor that makes their prices rise as much as they do is their brand name followed by the quarantining procedures they have in place which also helps continue their brand name remaining in good standing. Shipping is not that much, it's been a while since I paid for shipping from them but if I remember correctly I believe it was $30? Someone could fact check me if they wanted to. Free shipping used to be at $99.99 but now it is $149.99. Unpleasant that they raised the price for free shipping but understandable as they are a business.
Personally I myself find their prices to be horrendous for clown loaches to the point of never even considering them in a passing thought for buying clown loaches and I would advise others to do the same.