Great, I love you to start out FPGA clusters, there is only one possible criticism, it is wasteful to use a USB cable when two cables are only useful around the connector, I mean the input and output data, it may reduce the cost with the use of two simple normal pins and wires between the PCB and the hub.
Off the shelf is usually cheaper than custom.
If you create a custom wiring interface then you need a custom built hub. It is unlikely to be cheaper than a usb hub and usb cables. A 12 port hub is <$2.00 per port and usb cables in bulk are less <$1 ea. So cost becomes <$3.00 per unit (likely <$2.00 if you look hard enough). Maybe it is wasteful/overkill but it is unlikely any custom solution no matter how spartan will be cheaper than $3.00 per unit. Even if it is you are splitting pennies when you look at total system cost.