From my own experiences with panda recovery I found that adding noindex to low quality pages or product pages had no effect on recovery, whereas removing the pages or rewriting them to improve their content did have a positive impact.
From which I concluded that the existence of a material number of low quality noindex pages can cause problems i.e. that google still take into account the quality of pages when assessing a site as a whole even when they have noindex.
Of course, I only have a few sites to compare and other people might have different experiences - I changed many things on these sites as well as removing the noindex pages so it is difficult to know which solved the problem.
If your pages are high quality but noindexed for a different reason then I don't think there will be a problem for the site as a whole.