USB connector to BNC connectors back to USB connector
If your USB is working at high speed (480 Mbit/sec) rather than full speed (12 Mbit/sec), then yes: trying to split out the cable and run through BNC will give you all sorts of problems. The twisted pair in a USB cable presents a balanced load, while the BNCs do not. Worse, if your BNCs are connected to the bulkhead you'll have to use 2 BNCs, one for each data line. If the BNCs are floating, you can give it a try with both data lines through a single BNC, but be prepared for disappointment.