With Clipse, sure they had The Neptunes producing their albums. That's only part of the picture though.
Lord Willin', considering The Neptunes were THE producers that year only went gold. It had two big singles in "Grindin'" and "When's The Last Time". "Grindin" is legendary. "Ma, I Don't Love Her" stayed on MTV Jams. They also had the feature on "What Happened To That Boy". Lord Willin' only went gold. Is this Clipse fault? Nope. The Neptunes are among the greatest producers of all time, but their weakness was that they really weren't great at breaking new artists. They excelled at creating with already established artists.
Hell Hath No Fury came out at a time when The Neptunes were cooling off. Luda's "Money Maker" was a #1 and Gwen Stefani had a hit in "Wind It Up", but Pharrell's first solo album flopped commercially and that album was really dope. Even had Kanye on the second single. Hell Hath No Fury, as dark as it was, stood no chance commercially despite being produced by The Neptunes.
Til The Casket Drops suffered the same fate. It was a much happier album and "I'm Good" was like the Hip Hop version of "Happy" before Pharrell dropped "Happy". 2009, was a part of that run where The Neptunes were cold and we wouldn't see the return of Pharrell/The Neptunes at or near the top again until 2013.