Are dimpled chainstays weaker than smooth ones, other things equal? Here are two frames: Velo Orange Campeur and New Albion Drake. Assume that they are made of essentially the same steel, 4130 CrMo. The Drake has a very pronounced dimple on the inside, to help increase tire clearance. The Campeur, as far as I can tell, has no such dimple, so let's assume that the Campeur chainstay is entirely dimple-free, inside or out. Other things equal, would this difference make the Drake a weaker frame?
The dimpled chainstay may have less stiffness in certain directions at that point, but if forces are not concentrated there, or in the direction of less stiffness it just doesn't matter. 

A u-shaped beam (which is what the heavily dimpled tube essentially is) has less resistance to twisting forces than a tube, but there isn't any significant twisting forces on the stays.