I can attest to Amoeba's three locations continuing to sell classical titles, though "back in the day" they had a much more impressive selection, with the upstairs of the Berkeley location being all-classical. When I lived in Fresno, I worked at Borders Books and Music from 2000 to 2007 and the chain fell apart soon after. When I started there, I soon became in charge of the music (CDs) section. However, before too long interest in CDs declined from its 2000 peak and I found myself sorting and shelving all product lines. After that I would buy classical titles from Rasputin's, Amoeba's competitor in Berkeley although this outlet took over the space vacated by Tower Records in Fresno. Though they had a fairly large selection, they were almost entirely used (albiet at very good prices). That location is now called "Mad Monk" and its stock of recordings has declined severely.
The reality is that Classical music lovers have, for the most part, moved on to streaming. That article concerning the end of the Musical Offering didn't touch on how big an influence it was on the early music community internationally during its heyday thanks to Joseph Spencer. Unfortunately, Joseph Spence died in 2001 of a rare blood disorder and his influence was no longer a part of the store's reach into the larger classical music community. One era ended 25 years ago, the other last year.