Deduping 3,000 tracks by hand wouldn't actually take that long, particularly once you know whether or not the tracks are doubled up in Finder or only in the iTunes interface. Alternatively Dupin-Lite from the Mac App store might help you do it more efficently and isn't that expensive. Deleting everything from the library and then reimporting from the iPod is likely to make matters worse. Depending on the tools you use you will lose ratings, playlists, play counts, and still have to work out what media files might be in your library that aren't on the device so that you can rescue them.
Don't worry about the duplicates that have been there for ages to start with. What about all those that were created yesterday? Select a typical track and use Get Info then look at the file tab for the two copies of it. Are both copies pointed at exatcly the same path, or different ones?
tt2