A common problem I've seen with using onboard audio for advanced sound production is the audio tends to pick up noise from the other motherboard components. So most people doing serious audio work (and who are likely to use this connector) prefer external audio equipment which can be electrically shielded from the inside of the computer, and connected only via a USB cable (the digital link helps avoid ground loop issues).
So you've got a connector on the motherboard which both amateurs and pros don't want to use. Why would manufacturers continue to put it on? I dunno, maybe as a tie-breaker? If you're comparison shopping two motherboards and they're pretty equal in features, you may decide to pick the one with the S/PDIF connector even though you doubt you'll ever use it.