This has been highly dependent on the particular B&N, in my experience. One in Raleigh (may have technically been Cary, NC, this was 15 years or so ago) had Knuth's TAOCP on the shelves, never seen that anywhere else. Certainly not in towns with less technical inclination (a town I lived in in GA for a decade, for instance, had a miserable technical section) where the technical book section was dominated by Windows and MS Office how-tos.
University bookstores have (or had?) plenty of this. Like UW's bookstore or the engineering bookstore for Stanford. Haven't been to one of those for a long time, however.
By "the engineering bookstore for Stanford," do you mean their visitor bookstore, the one that has a cafe and sells branded campus gear like hoodies, mugs, and pennants? Yeah, it has a TAoCP box set on the shelf, but their tech shelf is otherwise pretty small, and far smaller than their entrepreneurship and business shelves, or even the "psychology and self-help" shelf.
No. The one that used to be next to DEC SRC near the Caltrain station…but that was 1999 or so. It was just a bookstore for the engineering school, so no hoodies or stuff, or books unrelated to engineering.
Given that the only parts of the Stanford campus that are near Caltrain today are some patient facilities and the arboretum, I suspect that this is something that has not existed in decades.
