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These pages are hidden in the sitemap, but there is consistent linking throughout the site where I'm unsure if we would be able to place a nofollow on the links, along with a few obscure places where other pages link to them.
If Google does find these pages, I wouldn't care if they slapped a duplicate content penalty on them since I don't need them to rank anyways. But, on the other hand, I don't want the fact that these pages have been penalized to have an adverse effect on the rest of the site. Sort of a guilty by association sort of thing; I know how Google doesn't like you to be anywhere in the neighborhood of spam.
Is this a valid concern?
If you want to safeguard, you could use a meta robots noindex in the head of the irrelevant pages.