I am sure over time, mudflaps will wear the paint behind them down, or at least scratch it. But why would you be removing your mudflaps?, the only time you ever would, Would be to replace them, right? so who cares if it messes up the paint behind them, your not going to see it anyway. I think nice mudflaps look 100 times better then chips all over your rocker panels, or that "Sandblasted look".
I have a Lund Bug deflector (The one that fits between the grill and the hood, no adhesive, so it will NEVER blow off or have to wrry about the foam adhesive tape failing). Alot of people bad mouth it becasue it scratches the paint. It DOES scratch the paint at the extreme front edge of the hood, but it is IMMPOSSIBLE to see it, unless you remove the bug deflector, which i never plan on doing. And like mudflaps, the bug deflector looks better then chipped hood paint.
What i am trying to say is, dont worry about hidden cosmetic paint damage if what causes it will be on your truck as long as you own it. Just buy a nice looking, well made product the first time, and you will never have to remove it.