I've read that the X79 chipset does not have native USB 3.0 support. However, I'm not entirely clear on what this means for performance, given that there are many X79 motherboards with USB 3.0 ports. How is the data rate impacted by this, if at all? Are there any other effects?
It would move the USB 3 controller out of the southbridge chip - which houses a whole bunch of different I/O devices - and onto something attached to another expansion bus. That would probably be the PCI express bus, these days, but theoretically could be something thinner.
Since the PCI express bus has more than enough bandwidth to support USB 3 speeds, odds are you wouldn't notice a lick of difference - but, it does mean that it would compete with anything else on the same bus, so if you start to push into the realm of bus bandwidth limits (between 250MB/s and 2GB/s) you might start to notice the difference.