You have this large site and you noindex a lot of the parameter, filter, sort, etc types of pages but yet, your navigation and internal linking structure links to these pages a lot – would that be an issue with Google and ranking? The short answer is no.
Google’s John Mueller told Laura Lippay, who is a seasoned SEO who has tons of large enterprise site SEO experience, that linking a lot to noindexed pages is not an issue.
I don’t see a problem with that.
— John ☆.o(≧▽≦)o.☆ (@JohnMu) April 20, 2018
Why would it be? Well, it might be considered sending mixed signals to Google. On one hand, you are telling Google with the noindex to not index the page for some reason and on the other hand, your internal linking structure is telling Google these pages are important to your users. So which is it?
In any event, John from Google said this should not be a problem – so there you have it.
Forum discussion at Twitter.