If the metadata of your files are identical, you should have the "Do not import duplicates" box checked when you import folders as projects. That should prevent most duplicates from importing.
However, if the metadata are different in any way, the files will import as two separate originals. I have yet to find an automated tool that will not make "mistakes" in cleaning up these duplicates, sometimes because the metadata of the old files are changed.
I am currently creating a clean repository of original images and doing any comparisons of conflicts visually in two File Finder windows before importing the "clean" folders of originals into Aperture. You can also import everything into Aperture first and then delete what you don't want, as Leonie describes. I just found File Finder faster for me to keep track of where everything was stored and what directories I was comparing.