I've delved into this somewhat in an attempt to get some badly-behaved USB cameras under control— the situation is not pretty, especially for USB 3 hubs. I ended up resorting us using a hub that had an internal jumper for disabling bus power, and then just using an external relay to toggle power to the hub itself and all attached devices.

This has worked fairly well, though it exposes some other interesting problems which I suspect are deeper issues in the Linux kernel, where "replugging" the same device hundreds of times over the course of days of runtime eventually exhausts some internal resource, causing the port to go completely dead until you unbind/bind the xhci device.

Note that if you're not on RPi or some other device with easily usable GPIO to control the relay, you can use any FTDI cable as 4x GPIO, and there are lots of cheap 5V relay breakout boards available.