Google relies on rel=”canonical” to merge all substantially identical URLs into a one canonical edition from the page. If a number of your canonicalised webpages use noindex you could be sending a blended signal to Google and there is a probability they may prefer to noindex the canonical version of the website page as well. We do not know the exact conditions less than which that is most likely to happen, nevertheless the general advice is always to minimize noise and be certain you are sending a clean concept to Google to forestall any undesired results.