As a former audio engineer who worked for one of the two famous German microphone companies, my intuitive thought is still to prefer S/PDIF over USB. Perhaps I'm just a dino who missed that all gear nowadays is equipped with USB. In my experiences a lot of consumer gear provides S/PDIF, but not necessarily USB, so assumed you one day want to connect your digital microphone to some other equipment (not to a computer), there might be no USB port available, while S/PDIF usually is available.
Actually, after reading the Wikipedia S/PDIF article it seems that S/PDIF does not have enough bandwidth for my purposes, since I am building a microphone array. Wikipedia implies that no more than 5 channels of PCM can sent over S/PDIF.