I had a similar thing happen a few years ago. I ran my rear wheel over a ring-shank roofing nail that went through the tire, both sides of the tube and punctured the rim far enough that the nail's point protruded from between two spokes. The nail was stuck so hard I couldn't remove it at roadside and had to call my wife to come and get me. I was really sick about it because it was a Campy Chorus 10-speed hub laced to a CXP-33 rim and was fairly new.

When I got home, I pulled out the nail and assessed the damage. Fortunately, the nail had missed all of the spokes and spoke holes. The tire was patched inside and still usable, the tube was a throwaway, the 3 mm hole in the inner wall of the rim was smoothed over and covered with Velox rim tape and the small hole in the outside of the rim was patched with silicone seal. The wheel is still in use over 10,000 miles later.