Zuhl3156
I set up a clothing shop for the woman who was married to the loser who ran that radio station. I gave her nothing to start with and out of nowhere she had suits, T-shirts and jeans, hats and numerous other things to wear. I just build a shop because it is supposed to make my settlers happy. I never give them anything to start out with. They are growing plenty of food to sell so I don't see a problem there. I might be getting paranoid but I have been worried about those Provisioners and their Brahmin stuck on that roof. I hope I don't get back to Egret Marina and find their skeletal remains. 
By investing caps into the shops you increase the amount of caps that they will have on hand which will raise their amount of caps the moment you do as well as for future selling.
Building shops does increase the happiness in settlements. I build the largest one of each shop. After that I will build the Food and Drink shop several times in a settlement. That one seems more productive than the rest of them.
All you have to do is drop a large floor platform between the rock ledge and the roof line. This will provide a path for them to leave the roof. Once I did this I have had no further issues with it. Leave the floor platform there once you lay it down.