I'd like to add a detachable shoulder strap to my waterproof panniers. I'm thinking of the kind of nylon shoulder strap with plastic clips that attach to a plastic loop or triangle sewn onto the bag. I've seen this kind of a mod on a pannier before, but I can't find any instructions or experiences of people who have done this sort of thing. I'm concerned about sewing something into a waterproof pannier. It probably won't be waterproof in that tiny spot anymore, but would that seriously compromise the bag and put my belongings at risk in the rain? Does anyone here have experience with modding waterproof panniers?

Most waterproof panniers have such loops. What material/construction are yours?

You should be fine....way back when I was in the boy scouts, we made our own waterproof backpack covers. If I remember it right, we used wax on the seams and then used seam sealer (can be bought in any outdoor section at wal mart or target or any store that sells camping stuff). We also always used seam sealer on any new tent. Seemed to do a pretty darn good job of keeping us dry.
Amazon.com : Gear Aid SilNet Silicone Seam Sealer Tube (1.5 -Ounce) : Camping And Hiking Equipment : Sports & Outdoors

I'm not sure what the material is, but this is the pannier: Avenir ACB940 Waterproof Rear Pannier - Red: Amazon.co.uk: Sports & Outdoors