tedster - 1:15 am on Sep 4, 2011 (gmt 0)
And I'd answer "yes" to your question. 90% of your URLs being noindex also sounds like a potential devaluation to me. I can't swear to this as 100% gospel, but I certainly don't know of any counterexample either.
Given the way Panda works, and Google's interest in rating the entire site by it's quality, I can only assume it would be an issue.