The reason for so many duplicate prestige classes is that,let's face it there are only so many major variations out there.
Everytime I get a new print publication I catalouge the prestige classes,spells,monsters, feats,magic items etc. So that I can find them easier when I want them later.I buy a majority of what comes out (though I'm looking at cutting back).But My point is that I count more than 500 "different" prestige classes in my collection of books alone.This doesn't count anything that is only available on the internet.
The only way the duplicate PrC are going to stop is if WoTC publishes some sort of Unearthed Arcana/Players Handbook II with the most obvious ones included and makes it open content immediately and although I can see the former happening probably next year the later probably isn't going to happen.