Hi There:
I'm not sure how you ended up with 54 catalogs, but I thought I'd muddy the waters for you a little bit. I tried importing my LR2 catalog into my existing LR3 catalog and Lightroom wouldn't do it. I tried converting the LR 2 catalog to LR 3 and then importing it, and I tried converting it on import, telling Lightroom to throw away the conversion after import. Neither one worked, so I dutifully submitted a report to Tom Hogarty's Bug Report form. I received an e-mail back saying that they discovered the bug after LR3 shipped, but Lightroom won't import a catalog if the catalog to be imported has the same folder(s) as the catalog into which you're trying to import it. As I mentioned, I tried converting the LR 2 catalog to a separate LR 3 catalog and importing that, and ran into the same challenge. I'm on Windows 7; I don't know if the Mac version has the same problems.
Now, you can tell Lightroom not to import suspected duplicates, so that may help you with your duplicate file names issue. Otherwise I believe it will label them as filename-2, filename-3 rather than overwriting an image that's already in that folder in the catalog. As far as developed images, unless I'm mistaken LR will use the most recent develop settings for an image based on the date in the metadata.
As far as not doing this again, you can decide on import how to import files (copy as DNG, copy, move or add), and you can also tell Lightroom where to copy or move the files if you choose that option. You can also add metadata and/or develop presets on import, and you can save those as import presets. The Import feature is really quite powerful.
Sounds like your assistant has some work to do.
Mike.