I support a bookstore or record store to stand on personal taste. But that is a 2 way street.
Niche marketing means you are limiting your audience.
I wouldn't expect a quality bookstore of any sort to stock "Rush Limbaugh Is A Fat Idiot" by Al Franken (I can find dozens of close-out copies at a number of bookstores that sell remained books) but obviously someone bought it at one point in time.
I am perplexed by stores that order 1 or 2 copies of something. Sell them immediately and never restock. This happens with smaller press magazines too (things with a 3 month shelf life can be expected to run out at the newsstand in 1 week). If something is a consistent seller, and you are not opposed to carrying it to begin with, find that right number of copies (or reorder) and meet the demand.
If I have to ask a bookstore to order me a book, often (but not always) I'll price search it myself online (at www.bookfinder.com). I'm already going to have to wait.
Some independent stores will sell promo CDs and sample copies of books they are sent. This may explain some of the "one of these things is not like the other" stocking policies. Or maybe the owner wanted to thumb through a copy but didn't want to buy his own.