I doubt it -- the number of users who use a Mac Mini as an entertainment center is probably so small Apple barely thinks about them. More likely is that HDMI has superseded the optical audio port for most users, so they save money by removing a port few use these days.
It's still a little weird. I think a lot of people would have a separate A/V receiver and speakers; maybe this is changing as old equipment gets replaced, but I suspect there are still far more homes with optical-capable A/V receivers than HDMI-capable ones.
This is just a standard annoying thing with Apple though. Their designs are very 'forward looking' in that they don't consider what potential customers already have so much as they do what their own future peripherals are going to need.
At this point HDMI is not a particularly new thing; my Marantz receiver from ~2007 had HDMI connections on it. Audio-only digital connections aren't necessarily going the way of the dodo yet, but they're becoming progressively more niche. So are home theater PCs, of course.
Anecdotally: I do have a Mac mini with my receiver, which I replaced this year. But the new receiver not only has USB input, it has wifi and built-in clients for Spotify, Tidal, Pandora, TuneIn, Roon, whatever protocol Windows uses for media sharing whose name I'm utterly blanking on right now, and a dozen or so other services, with Apple Airplay 2 theoretically coming in an update.
