Should we have one "sys-usb" per USB Controller?

I thought that I should just reply in order to help those who use search and get here.

Yes, such approach goes along with the main point of Qubes OS: security through compartmentalization.

Yes. However, it also depends on your threat model. For instance, if you have some USB device as trusted as the keyboard, you could also use it on the same USB controller as the keyboard.

Yes, people are doing this.