The Hidden Price of a Christmas Bestseller lays out the fees involved in getting books promoted in English bookstores. Similar set-ups exist here in the States. In fact, this practice is supposed to be one of the reasons publishers are taking out fewer ads in U.S. newspaper book review supplements, which is said to be one of the reasons those supplements are folding. Publishers are shifting their advertising money to paying to have books promoted in bookstores instead of taking out traditional advertisements.
I think this isn't considered a questionable practice because the publishing industry has accepted it. Bookstore chains probably have employees whose entire job is to sell window and table space to publishers. Publishers probably have employees whose entire job is to buy window and table space from bookstores. Heck, both groups probably have entire departments to handle this stuff.
My guess is that if both buyer and seller agree that something is an acceptable business practice, it's an acceptable business practice.