Hey penguinpimp, thanks for the promo!
Basically I agree with your summary, it's partly cost, and partly ignorance.
A tropical fish store isn't a public aquarium. Retailers want to shift their stock as quickly as possible. Live fish are expensive, and the longer you keep them, the less profitable they become. Why? Because unlike, say, dry goods or books, fish consume energy (heat, filtration) and resources (water, food). Obviously any fish that die is money down the drain. In fact for many stores the fish are 'loss leaders' -- they may bring in the customers, but the profit that keeps the store viable is from the tanks, fish food, ornaments, etc.
So, what the retailer wants to do is get the fish sold as quickly as possible. This is why small stores tend to focus on 'bread and butter' species -- goldfish, guppies, angels, and so on. There is a consistent demand for these fish. Brackish water fish are specialist fish, and the demand is not predictable. The bigger stores can afford to keep them because they attract more buyers, of whom some will be looking for specialist livestock.
Ironically perhaps, many species would do better if stores kept them in the marine tanks rather than the freshwater ones, yet many retailers do seem to keep them in the freshwater tanks. But they are at least hardy, and rarely would I hesitate to buy a brackish water fish just because it's currently in a freshwater aquarium. Provided you know what the fish requires, and the fish you're interested in are feeding and healthy, I wouldn't worry too much about the fact the stores are keeping them badly.
Cheers,
Neale