We struggled to find a better cover than the recommended one from Kauailabs so we decided to design our own. It can be printed with no supports and mounts with two #4-40 1/2" long bolts directly to the RIO. We like these Torx screws from McMaster.
We have never needed access to the USB port. If you need access you can pop the two screws off temporarily, or feel free to modify our design. Our main goal was to block off any dust or debris so we made sure everything was fully enclosed!
The USB port is definitely useful, as it can act as a secondary source of power for the NavX. The MXP port is one of the first things the roboRIO cuts power to during a brownout. The USB ports on the RIO however are not turned off, so they can keep your NavX running when it normally would have rebooted.
So we communicate to our NavX over MXP, but we have a USB-A to mini-USB cable going from one of the roboRIO USB ports to the mini USB on the NavX.