After upgrading to Aperture 3 I had to 'upgrade' all files. When this was done, there was an Aperture 3 library and the original Aperture 2 library. Are the two libraries identical and can I safely trash the Aperture 2 library?

If the upgrade completed successfully and you are running Aperture 3 on the converted library and you're sure all the images that were in the old library are in the new library then you could delete the Aperture 2 library.
However I'm the paranoid type and when it comes to deleting images I'm always hesitant. If you can fine a place to archive the old library that would be your a better option.
At a minimum I would keep the old library around for a month or so after switching to Aperture 3 just to make sure in case something pops up.
regards

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