This is one of those mysteries that may ultimately go unsolved. I can give you some pointers on locating the music, assuming it's not lost forever. I can also assure you that you are not doomed to a life of randomly disappearing music files- they went away for a reason.
There was one thing in your letter that raised a red flag: You mentioned cleaning out duplicate files. Is it possible some of you music files could have been caught up in the sweep? Did you use a program to find duplicate files or use your own judgment (both have the potential for error)?
When you say missing songs, it could mean one of two things: Missing from your Windows Media Player library or physically missing from the hard drive. If they are missing from the library, you can simply add them back (once you find them). If they are missing from the hard drive, they may be gone for good.
Here's how to search your entire hard drive for your missing music files. From the Start Menu, select "Search." When the Search window appears, click "All Files and Folders." Finally, type in the name of a song you are missing in the top text box that reads, "All or part of the file name" and click "Search."
If your files show up in the search, they probably just went missing from your Windows Media Player library. Right-click the music file and select "Open Containing Folder" to see where these files are located on your hard drive. You can drag the music files right into your library.
If your search didn't turn up any missing files, your last resort is the Recycle Bin. You may find some, if not all of your missing files in there. If you do find them, the "Date Deleted" may clue you in to how these files were deleted. (What was I doing that day?)
Good luck to you. And get that backup system in place as soon as you can. The more you play around with your music collection, the more chances you have to mess something up!