It doesn't hurt them and some of mine will even sit still for it! I have a 4' chain link fence on either side of my yard and live in the middle of a city- so it had to be done. They don't mind, and it keeps them from hopping fences.
I have a 10'x10' playhouse 3' off the ground under which they can run if something flies into the area, and various shrubs and stuff they can take cover in throughout the yard. No daytime ground predators can get into the yard, and they have a pre-fab 8'x8' garden shed for Fort Knox Coop at night.
If if keeps them in your yard, it's a good idea, IMHO. If mine got into our North or West neighbor's yard, they'd be one more fence hop from 3 or 4 fenced-in pit-bulls. I'd hate to see that. I clip *because* I love them!