Only HQCT eA is connected directly to the mini. All the remaining devices are connected using two hubs (in a chain) and the power of these hubs is completely isolated from the Mini. And AFAIK there was never any problem with recognizing the devices - either on my PPC or on Intels of my colleagues and a few customers.
As a matter of fact the only two USB devices causing problems are USB modems for CDMA (EVDO-1?) and 3G (Huawei E220). These sometimes just stop working and need to be re-plugged, sometimes they disconnect so long that sleep or shutdown attempts can't be completed etc.