For your case, do what USB hosts like PCs do - connect shield to ground at host, and let the USB devices do what they do.
If you look at a standard PC as an example, the connector on PC motherboard or front panel will have the connector metal shell connected to chassis ground, and on the USB cable the connector metal shell connects to the cable shield.
The USB cable itself has the shield connected to metal shells of the USB connectors. Therefore it is up to the USB devices to define how they connect to the cable shield, if at all.
Many USB devices do not connect ground directly to shield due to electromagnetic emissions and signal integrity issues. Some might use a capacitor or ferrite bead to connect to the shield, or it may be directly connected or left disconnected - it depends on many things such as what device it is, does it have a separate mains supply or not, or does it have external connections to other equipment or not. So the best way to connect the shield depends what device are you making - a mouse, a printer, or an Ethernet dongle
But on a simple case of just being a simple USB host, they typically connect the connector metal case, i.e. the cable shield, directly to USB host ground.
So in this case, you should connect the USB cable shield to SBC ground directly.