I'm not sure about USB 3.0, but SATA 3 for sure will decrease the speed of the VGA to 8X because it shares the same PCI-E lanes. Also the SATA 3 speed isn't the full 6gb/s. It's probably around 4~5 GB/s.
If you want full speed. ASUS has a new revision of their Maximus III coming out soon with the NF200 chip to allow full speed SATA 3 and GPU.
to help the others who wants the answer
I asked Gigabyte technical service and they answered me:
Thank you for your kindly mail. GA-X58A-UD3R does not have such limitation, if you only have one VGA card, the VGA card, SATA 6Gb and USB 3.0 will work in full speed.
I hope this helps someone
Yes, this is true for the X58 boards, but not the P55 boards. Without the NF200 chip, the P55 boards are limited to only 16 lanes of PCI-E....which means...youc an CFX or SLI without SATA3/USB3 or you can have one VGA running at 8X with SATA3/USB3 or you can have one VGA running at 16X (the best option)