I guess you mean it doesn't support apple's built in digital outputs? I use VLC through my MOTU 2408mkIII all the time running 100% digital with no problems ...
Another thing I've noticed as well, is that VLC can even request the hardware to change sampling rate from 44.1k to 48k
![Wink ;)](./images/smilies/icon_wink.gif)
While at times this has caused me grief it is the proper behavior