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Why not use firewire instead? Or use a NAS drive (which is what I use)?
But ... both ports are shared with the iSight camera? You want to double check that? There really should be one powered, and unshared / exclusive USB port. The unpowered one you could just augment with a powered USB hub and plug your external drive into it, although you might be better off with a self powered external drive rather than rely on USB power.
Whether it outperforms your Airport Express or not, it may very well have nothing to do with whether the USB controller is shared or not. Personally, I have found that bigger differences are found in quality of USB to SPDIF converter, quality of DAC, the audio player (iTunes, PureMusic, Audirvana+), etc.
In other words, in terms of priority, if you find you aren't happy, perhaps spending $700 on a new Mac Mini would be less effective than, say, trying Audirvana+, upgrading the DAC, or replacing the Hiface. But, to be honest, I'm somewhat blind here because I don't know what the rest of your audio system looks like.