This is certainly odd, as it doesn't really match the experience I have with my local B&N. I picked up the last two TOS novels fairly easily. Trek commands about 1 and a half shelves at my store, with about 5 shelves for Star Wars. Allegiance in Exile was prominently displayed on the new SciFi shelf today when I went in today to get the new RA Salvatore book, whereas Devil's Bargain was "hidden" in amongst the older Trek releases. I ended up getting both books the Friday before they were released. There were probably about 8 or 9 copies of Allegiance when I bought it. I think there were maybe 6 of Devil in February. Today, there were 3 copies of Allegiance (one of which was mixed in with the Star Wars books) and two copies of Devil.
The selection of Trek books is a bit odd, though. It feels more like "What wouldn't sell" then "Popular." No destiny books, after about 6 months most of the "recent" books are gone. Currently Death in Winter, the first two Titan books, a host of Troublesome Minds and the odd book from the last four months populate the shelves. DiW is the oldest book on the Shelf for Trek, and it does in fact look it. Though, I did find the DS9-R Mirror Universe trilogy there last year.
There's also a Trek Lit standee right at the front of the store with the latest Typhon Pact novels. So either this store didn't get the memo about the distributor tiff or they don't care. There is another B&N not too far from me, but they're smaller (one floor vs. 2) so their SciFi selection is meager to begin with, with Star Wars having two shelves and Trek sharing a shelf with Torchwood and Doctor Who.
Granted the experience of one store doesn't equate to general trends, but I find this most perplexing. And to deflect the e-book question, I really only get Trek-back catalog books for my Kindle, the newer releases tend to be much easier to get a hold of.
(On an even odder note, the B&N at Lincoln Center in NYC had a full shelf of the BBC's Doctor Who novels in 2004-2005 which disappeared once the new series started and they didn't carry the novels until late in Tennant's run!)