USB is an engineered interface which has a fixed set of specifications. Those devices which match the specification will work fully and without issue. Those devices which do not meet the specifications are not allowed to use the term USB or to display the USB logo. However, things are not always that simple.
This means that audiophile grade USB cables are complete and utter tosh. It doesn't matter if they by dint of overengineering actually surpass the USB spec by any manner, because the interface will not gain anything from it. If however the cable company has just cobbled together something which happens to have a USB connector on each end, and between them lies a hosepipe with MOAR SILVAR, then yes, thats expensive, but does it actually do the job its designed for as well as the cable that came free with your printer?
There are lots of things that don't meet the spec in some way or another, devices that try to draw more than the maximum allowed power from the bus for example.
Your motherboards USB sockets are just the same as the ones on your laptop, nominally. That is to say with portable devices like laptops, or anything which might run off a battery, there are compromises, for example, the USB sockets on laptops might only offer the base level of power output for devices, this means charging will take longer and daisy chaining things to that socket will sooner require the use of a powered hub than it otherwise might.
Another consideration is overall USB bus traffic. If you connect an external hard drive with yoru music on it to a different port on the same USB bus as a USB DAC, then the data is travelling both into and out of the same bus after processing, this can cause dropouts, espeically if the DAC is powered from that bus directly. I ran into this very problem at the UK meet recently because my netbook has all of its USB sockets on the same bus and I didn't use an external power supply for my hard drive or USB transport.
As for mechanical hard drives inserting noise into the USB bus and corrupting the sound output. That's a bunch of complete rubbish. If mechanical hard drives had been causing that sort of signal problem for external connections it'd have been a massively well known issue and quickly resolved. Thats assuming that the issue could ever come up in the first place.
In short. Don't worry about it until the point where a problem actually arises, then ascertain what is causing it. Hope this helps.