Google’s John Mueller addressed the topic of page pruning again, but this time explains that Google can only judge the overall site quality based on the pages they have of that site that is in their index. So if you block Google from crawling and indexing sections of your site via noindex, nofollow, Google won’t consider the pages that are not in their index for the overall site quality.

John said this at the 20:05 mark into a video hangout from earlier this month:

Question:

Answer:

But John goes on to explain that in this case, it probably makes more sense not to block the pages but to use the rel=canonical attribute to point those signals to a single page, instead of just killing off the page totally from Google. John added:

Glenn Gabe has an awesome tweet and GIF summing it all up:

Here is the video embed:

Forum discussion at Twitter.