Agreed, there is way too much flex between the bed and the cab- you'd end up ripping something loose. I've seen racks mounted on the cab and the shell, racks on one or the other and then ladder rack styles mounted on the bed walls that extend over the cab. As for mounting a rack to your camper shell it's entirely possible depending on the type of shell, where you mount it to the shell and how much weight you intend to carry. I've got a Yakima rail rider system with 66" bars on my ARE shell and I've carried several boats up there at a time with no issues.
The key is to get a decent shell that's rated to carry extra weight then properly mounting it. A lot of the shells out there these days use a honeycomb material in the center- you do not want to drill through that as you can't get your fasteners tight without damaging it. Also, don't put too much weight or anything that's going to cause too much updraft; when carrying canoes I always run bow lines to the ARB bumper so any upward force is on the bumper, not the rack. Remember that any weight up high negatively effects your center of gravity too (and anything up there negatively impacts your fuel economy).