If memory serves, the update from 2.x to 3.x was the one were suddenly skins no longer worked and they decided to base the program around a db instead of the file system. Which is not that bad (though still strictly inferior to file based) in modern cell phones, but at a time when computers were a lot slower and everybody had organized their music library around files instead of metadata it was a bloody disaster.
I dunno... Libraries were a revolution for me. If I remember correctly, that was around the time I briefly switched to iTunes for its library features. The ability to start typing and instantly see a list of song matches was great. The problem with the WinAMP library was that it wasn't that good. If course iTunes turned into a bloated mess too, and I ended up on foobar2000 for years.
JWZ's hate of HN is long-running and due to a combination of factors, but I reckon his real annoyance is the amount of traffic this site can send to his little servers.