For the sam3x8e (arduino due), the default arduino code driving the USB communications is the main limitation on the native port,
https://www.pjrc.com/teensy/benchmark_usb_serial_receive.htmlWhile I was researching for my own project in the past I found many implementations able to handle SD card - Native USB at up to 20MBps, but I never got to programming up that project.
as you are saying you want it to act as a "USB Bridge" you should be aware only 1 of the USB ports is native, the other is relying on a UART-USB chip, he will be your main limitation.