Earlier quoted context omitted.
Now that I think about it, axing the optical audio ports was probably a deliberate move by Apple to nudge home TV users of mac minis into using Apple TVs, where they have way more control over the interface and content. edit: apparently Apple TV doesn't have optical audio either.
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 More likely is that HDMI has superseded the optical audio port for most users, so they save money by removing a port few use these days.
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.