Concurrent sound limits still apply. That's the amount of digital sound samples that the sound card can mix into one signal on-the-fly.
S/PDIF only means that the digital signal is sent directly to the speaker hardware through digital connection, where the on-board amplifier does the conversion from digital to analog and plays it through the speakers.
With analog speakers the signal is first converted to analog on the sound card itself and then simply given to the analog speakers to handle.
Here's the rub: DAC quality matters quite a bit with digital audio. So basically if you are looking for ideal sound, you would probably want to optimize the digital to analog conversion quality.
If you are using analog speakers and on-board HD audio chip, what happens is that the onboard DAC will have to do the digital-to-analog conversion, and it usually doesn't do half as good a work as the DAC in-built in a speaker setup that has S/PDIF input, and definitely nowhere near the DAC quality of a dedicated soundcard.
That means that you will definitely get better sound quality if you use a dedicated sound card with analog speakers, or with headphones - because the DAC quality in a dedicated soundcard is typically very much superior to onboard audio chips'.
However if you happen to have digital speaker setup (like home stereo), and you choose to use that input option, then the digital to analog conversion is done in the speaker amp hardware itself. What this means is, quality-wise it doesn't matter whether the digital audio signal comes from onboard HD audio chip or a dedicated sound card. Digital signal is digital, so as long as the onboard card is capable of producing the same digital audio data, the output from the speakers will be identical.
Where you can have differences, then, is what the actual stuff in the digital audio signal can have, if you're comparing onboard HD audio chips with a dedicated sound card. Typically, like Fury mentioned, dedicated sound cards have more processing power and can handle more bit depth, higher sample rates, more concurrent samples (which is quite important in gaming) and they also usually have better support for things such as speaker virtualization (downmixing surround sound to headphones so that it still sounds like surround, for example).
So, dedicated sound card can still give you better sound in some cases even with digital speakers, but if you for example play CD audio (44kHz16bit stereo PCM wav) through your onboard sound card and dedicated sound card, and you use digital speakers - then there should not be any difference at all.
...except for the fact that if you use something like ASIO instead of Windows Audio Service, you'll get better sound quality, because windows audio service doesn't preserve the waveform, while ASIO does it exactly bit-wise until conversion to analog signal. And if your sound card supports ASIO (or equivalent bit-wise playback mode) you don't need to dick around with workarounds to get that working (ASIO4ALL works on pretty much all sound solutions but is somewhat more fiddly than driver level supported ASIO).
Also something to note: If your dedicated sound card has a better DAC than your digital speakers, you might actually get better audio quality by letting your sound card do the digital-to-analog conversion, and using analog cables to output the signal to your speaker setup.
Yes, digital signal is practically immune to interference. Yes, technically you should want to keep the signal digital as long as possible. However, I for one wouldn't automatically trust that the DAC built in the speakers can do as good a job as the sound card on my PC, so I would probably at least test things with S/PDIF as well as analog cables. If there's no palpable difference, then the digital cable is (obviously) a lot more convenient.
Also, with the advent of HDMI cables, most GPU's these days also double as sound cards. Granted they probably don't have very glorious list of options, but they definitely are HD audio devices, and they output the sound via HDMI connection so if you are looking for the most reduced amounts of cable hell, that would probably be your pick...