The digital audio output (assuming it's not broken) will output whatever your source is. If that is Dolby 5.1, it will be 5.1. Note that some software does not support 5.1, like Quicktime. But add-ons do, and so do other software programs like DVD Player. (I hope I don't have those reversed)
I have tested this with my Mini, and it works perfectly. Including 6.1 from certain DVDs. My receiver reports what signal it is receiving from the optical line, that is my proof.