Commenter John Topley wondered why clearing document history also clears Run history. Simple: Because people wanted it to.

Originally, the button merely erased your recent document history, but with the increasing paranoia over what records the computer kept on your past usage, people began to expect more and even filed beta bugs saying, "I cleared my document history, but I went to Location X and the names of documents I used recently was still visible."

I guess these people were afraid of being raided by the F*I, or more likely (but nobody will admit to it) by their spouse.