I saw someone suggested on here getting longer bolts for the rear fender and installing them from the back side and then securing them with a nut from the outside so that when you are removing and reinstalling your saddlebags you only have to remove the nut and don't have to fuss with trying to align the holes in the fender and weld nut from the backside. (sorry for the long explanation)
I don't see why you couldn't use this same principal to accomplish what you are asking about with the sissy bar, especially if you have saddlebags, you would just have more stud sticking out when the sissy bar isn't on the bike but since most sissy bar brackets are a little over 1/8" thick, it wouldn't be much more sticking out.
I found longer 10mmx1.25 bolts at Lowe's and am going to try this when I get my taller sissy bar in.