I don't work for Apple and I'm not a programmer. I'm just another frustrated user like you.
That being said, this is my experience. Maybe it will help you find your music, maybe it won't. No harm, No foul.
In the past I've always had good luck with iTunes. Then I downloaded iTunes 11.
Twice now my entire library has gone missing for no apparent reason.
While looking for my music I discovered that in my "iTunes Music" folder there were folders with the names of artists whose music I had downloaded from eMusic. These folders were (like yours) empty. The music tracks were actually in my eMusic folder. I don't know why iTunes created a dummy folder for them. It seems to have only happened with music that I had bought (from eMusic) a while back. The newer stuff I bought was just put in the eMusic folder.
As for CDs that I have ripped myself, I have found that iTunes puts them in the "iTunes music" folder under "Music". Just look down the list of artist folders and you will see a folder called Music. This is where iTunes puts all music that I have ripped. If I was looking for a Billy Joel album the path would be...
C:\Documents and Settings\My Documents\My Music\iTunes\iTunes Music\Music\Billy Joel\Storm Front
Clicking on the Storm Front folder would reveal the track names.
To add the tracks back into iTunes use the "Add To Library" in iTunes and follow the path to the artist/album you need to add.
Yes, it's a hassle. But it has to be done to get your music back.
I hope this helps. Good luck.