That is a huge and abnormal delay. I suspect there's a problem among the device drivers involved. First, check with the Tech Support guys that made the mouse etc. and ask whether their product has any problems with a USB3 connection, instead of USB2. I'm thinking their drivers may expect to find it on the USB2 bus and take too much time to find its real location.
Next, try this method to get rid of the related device drivers and re-install them to force them to discover the real connection paths.
1. Go into Device Manager and delete the driver(s) for the mouse. Maybe this is called Remove This Device.
2. Then do the same for the USB3 hub device.
3. Shut down and disconnect both those devices. Now boot up so the system is forced to recognize that neither of them exists.
4. Shut down, re-connect only the USB3 Hub and its power supply, then boot up. The system should detect that the Hub has been added as a new device and re-install its driver(s).
5. Shut down again, and plug the mouse back into the Hub. Boot up, and the system should find the new mouse and re-install its driver.
Now, does that make any difference?
If that fixes the mouse problem but not the similar delays with the keyboard, try doing the same idea for it. That is, remove the keyboard driver but leave the Hub in place, boot up so it recognizes no keyboard exists, then shut down and re-attach and reboot so it finds the keyboard again and re-installs the driver.