There was a huge thread on people having issues with the usb ports on their Thunderbolt 3 dock randomly not working. Lots of comments about updating drivers, etc...but no consistent resolution. I couldn't reply there so figured I'd post the fix here.
It's pretty simple, and I saw it in the troubleshooting guide for it. For whatever reason, sometimes it just doesn't link up to it. Good practice is to either remove the dock, then shut down. Or shut down, then remove the dock. Going into sleep or hibernate mode and THEN removing the dock (or connecting it when it's already in sleep or hibernate) seems to cause issues.
If something happens and you notice the USB devices connected to the dock aren't showing up, shut down the computer, and then push the button to restart but hold it down for 15 seconds to perform a "hard reset". The lights will flash for a second and then go dim again. Then push the button normally to start it up and everything will work fine. I've had it work in less than 15 seconds but may be depending on your specific system. This temporarily disconnects the internal battery to fully reset the computer. Then it'll find all the USB devices connected again.