Reference or Library? Which is better for the long run?

I decided to waste a day and re-organize my disorganized database of photographs held within aperture. I don't have any experience with referencing files but I was considering whether there are pros and cons to having files externally referenced versus having them within the Aperture library.
My habits are non-routine and I shoot pretty much anything, so I'm looking for a system that will ensure my library is flexible, stable, and safe for future use and access.
I suppose the only reason I can think of for referencing is having some control of where the actual files are so I can access/refer to them with other apps.
Please share your thoughts, experiences, and preferences.

I guess you are right about the duplicates still being an issue even if you find them outside of Aperture, since you still need to delete the links within Aperture, correct?
I never really worked with migrating projects except for moving the sample projects out to save space.
I was trying to think of how I will manage a RAW library when I can get my hands on that equipment, but migrating projects doesn't seem like such a bad thing to do. In fact, it seems rather ideal. Most of the time, I only need access to certain projects in certain parts of the year, and the rest of the time I never touch the photos.
You all have convinced me to give the managed library another go as I restructure my database. But I am still looking for the best ways to catch duplicates within Aperture. I know that you can stem them upon import, but Aperture's import duplicate-recognition technology in not consistent at all for me. Photos can be exactly the same but if they were not imported from the same source (i.e. memory card vs. finder folder) then Aperture won't think anything of it.
This is off topic, but is there a way to customize Aperture's duplicate detection? You would think that a pro software (and Aperture is pro, right?) would allow this. I might start a new thread on this topic.
The reason for my current obsession with duplicates is that I have a library of 12.5 GB of photos that I am pretty certain are already in Aperture, but when I test an import with the check box for not importing dupes, Aperture considers all the photos new. I then go in and find that none in that folder are new, but instead that they are all already in Aperture as is. Granted, I'm not worried about dupes taken after my migration to Aperture but for all of my photos before then, I'm kind of in a bind still.

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