Will setting noindex/nofollow on parent pages affect site SEO for child pages?

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This is a two part question.

Each parent page to link to the first Child page. They parent pages will not have any content. They will serve as main menu links, site URL structure and site hierarchy. My website(wp) structure is as follows:

  1. Home
    • Parent 1
      • Child A
      • Child B
      • Child C
    • Parent 2
      • Child A
      • Child B
      • Child C
    • Parent 3
      • Child A
      • Child B
      • Child C

Questions:

  1. If I set the parent pages to noindex, nofollow, and remove them from my sitemap, will this affect the child pages SEO?
  2. Will setting the main-menu(parent pages) links to the child pages affect my SEO?
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It will all have an effect on your SEO. If you don't explicitly allow the child pages in the robots.txt file you will have a site that is not crawled at all by the search engines (the ones that obey robots.txt at least).

In robots.txt to get any traffic from search engines you need to set the code to:

User-agent: *
allow: /Parent 1/Child A
allow: /Parent 2/Child A
allow: /Parent 3/Child A

allow: /Parent 1/Child B
allow: /Parent 2/Child B
allow: /Parent 3/Child B

allow: /Parent 1/Child C
allow: /Parent 2/Child C
allow: /Parent 3/Child C

User-agent: *
Disallow: /Parent 1
Disallow: /Parent 2
Disallow: /Parent 3

The sites will still crawl the pages and use them to rank pages, but they will not however rank pages set for non-indexing in the search results. They will rank any pages receiving links from those pages.

Basically the search engines have to look at every page to make sure you're not spamdexing or doing anything against their terms of service.

You have to be careful with these settings because according to Google:

To prevent all robots from indexing a page on your site, place the following meta tag into the <head> section of your page:

<meta name="robots" content="noindex">

When we see the noindex meta tag on a page, Google will completely drop the page from our search results, even if other pages link to it. Other search engines, however, may interpret this directive differently. As a result, a link to the page can still appear in their search results.

Other notes

Basically the search engines want to provide an end user with the link they were searching for. They check this by following users through browsers, cookies, analytics software, and other various things like plug-ins, links, referrals, and links from the page for relevance in content. By placing a page in their index with keywords in the content, where those keywords do not deliver the person to the page they were looking for, you run the risk of the visitors "bouncing" if the page is not relevant to their search. If they bounce then the search engines (mainly Google) will not think the page is relevant and will down-rank the page (and subsequently the site).