I really wonder :
- WHY they removed it
- WHAT they precisely removed from the BBB PCB

Removing a connector, or having a special run of BBB without the connector, adds complexity to the process.
If KnC did that, they must have a really serious reason.
Or maybe there was a shortage of USB connectors, but I don't believe this.

If they removed only the connector, AND there was no reason to remove it (unlikely), then it should be easy to add a connector and plug a USB device.
If anyone feels brave enough to do it, let us know how it turns out

Same for the mini HDMI connector, it looks like it's been removed : it would be nice to connect a small LCD screen to show cgminer.
It might require some small changes to the firmware so that the "screen" process running cgminer outputs to the framebuffer, but that can be done.

I'd love to work on all this, but I need to get my miner first.