This reply may be late to the party but, for prosperity's sake, I hope it may help others who encounter this issue.
A client's Mac Mini 4,1 already had 2 non-working usb ports so I installed a powered 4port usb3 hub. Afterwards I updated the OS from Lion to El Capitan 10.11.6 to accommodate updates to Skype. This is when I encountered the dreaded notification. I tried the usual: reset SMC; NVRAM; safe-boot; check the firmware, which was up to date; visually inspected the ports for damage, nothing obvious could be seen; unplugged all the usb devices and plugged them back in individually in the 2 working ports–all to no avail. I looked through the console logs and found that the usb port throwing the error was one of the dead ports which made sense since all the peripherals were working normally, it was only the notification that would not go away and was a causing slow down to the system. Like everyone else I scoured the net for a resolve and my last resort was, as mentioned here, to turn off notifications; which was not an issue with the client. The difference is I did it through the terminal with the following code found in another forum. The notifications have stopped and the mac is running smoothly now. What I haven't done, yet, is turn it back on...maybe next time I am called back I will do that and report back. Here is the how:
Use this code to disable the User Notification Center plist for about 1 hour without shutting down:
sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.UserNotificationCenter.plist
Then re-enable with this code:
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.UserNotificationCenter.plist
As always any code applied in the terminal is done so at your own risk.