I use DDU every time I install a new driver and I've never had an issue with it, going back years now. Unless your Windows install is inherently broken somehow, there's no reason why there should be any future problems after using it. The entire point of the program is that it cleans out everything driver-related so you can start fresh, free from any potential conflicts or issues caused by cruft from old installations.
This.
I've also used DDU countless times. Never had an issue.