Yes, all the aluminum frame Honda's do get wear spots in the frame sparts where the shroud touches, and where the steering stops come to rest on them. Thats cuz aluminum is such a soft metal. One trick I did on my CR, is to put electrical tape on the spares right where the radiator shroud rubs against it. It did the trick. Also, as far as the radiators bending, I believe one of the first mods to be done to any bike, are the "insurance" mods. Such as, the Devol radiator guards. I believe they are like $66 right now, and that beats having to buy a new radiator for $185, or the hassel of having your radiator repaired.
Then the rubber bar mounts... yes all rubber bar mounts are prone to bending the handlebar mount legs. They allow too much flex, and provide a weak point for the top clamp legs to bend, or become tweaked. One solution is the RG3 clamp, that has a 4 post rubber mount system. But that's expensive at $289 I believe. One of the best clamps on the market though. Otherwise you could do like someone else mentioned and make them solid mounted. Rubber mounts have their pro's and con's like anything else.