Maybe it's a "chicken and the egg" type of situation. There's less Star Trek books on the shelves, so less people are buying them. And because less people are buying them, there's less reason to have Star Trek books on the shelves.
As mentioned before, Trek books are still showing up on bestseller lists from time to time. People are still buying them, just not so much in brick-and-mortar stores. Looking over my sales figures from S&S, it looks like e-books account for over 40 percent of sales on my last few Trek novels. And though I can't tell from the provided info, I'm sure a large percentage of the print copies sold are going through Amazon and other online retailers rather than physical stores.