So I ended up importing the same files several times into Aperture, which merrily adds dupes without prompting. After googling around a bit and determining that I was not the only one with this problem, and not finding a real solution, I am posting my workaround in hopes that someone has a better idea.
I threw all the projects I knew had dupes into one big project with about 5,000 photos. I then exported these with the masters option, and used the subfolder format of ImageYear/Month. This took only a minute or so. When you have a file such as DSCN1591 multiple times, it will append a (1), etc. to the dupes.
I then did a spotlight search for the "(" (you have to use the quotes to find the paren) and deleted all the dupes. Then I re-imported the new slimmed-down photos. Someone please post a note with the menu option that does this that I didn't find...
Mac OS X Hints
http://hints.macworld.com/article.php?story=20071222002718187