See "Moonport", NASA's official history on the creation of the Cape Canaveral facilities, focused primarily on Apollo, for a detailed discussion of why Canaveral was selected. It also discusses the pre-Apollo Canaveral developments in brief. Shuttle operations were built off of Apollo infrastructure (VAB, LC-39 A and B, launchers, crawlers, etc.).
Even in 1961, with all of the Mercury, Air Force, and potential Gemini infrastructure in place, there was still a pretty good chance that Cumberland Island, GA, could have been selected for the Apollo launch facilities. Other locations were also considered. See chapter 5 for all the details.
http://www.hq.nasa.gov/office/pao/History/SP-4204/cover.html
Don't know about the Shuttle, but the Apollo 13 lunar module had a few pounds of plutonium on it when it came back to earth. Usually, the LMs were left on the lunar surface (descent stage) or in a lunar orbit that eventually crashed into the moon in most cases (ascent stage - see Apollo by the Numbers for the gory details on location, energy, etc.). Apollo 13 had an experiment that was powered by plutonium decay, and was going to be left on the moon, but when the LM was used as a "liferaft", it was flown back to earth, and only discarded before reentry. The LM, including its plutonium, ended up in the ocean (at least the parts that didn't burn up, including the plutonium,which was in a graphite cask, and sunk in 20,000 feet of water).