Given that Grammy's didn't really give out hiphop Grammy's until like 96, I can't name a year that he should've won.
It's like wondering why Carl Malone never won an MVP, longevity or being a legend is not what they are trying to honor here.
So really he's never been snubbed. He had strong singles like Drop it like it's hot, but they lost against even stronger singles like Jesus Walks (and 99 problems, Hey mama), or Beautiful vs Eminem's Lose yourself (and In da club and on). Grammy's is about peaks, just like the MVP.