Homepage has Paged Pages that should not exist, like /page/2/ and on to /page/99999/

To remove relational links from the single post <head> use

remove_action( 'wp_head', 'adjacent_posts_rel_link_wp_head' );

adjacent_posts_rel_link_wp_head documentation.

To return Status 404 on paginated pages use .htaccess rule similar to following:

RewriteRule ^page/([0-9]+)/$ http://yourdomain.tld/404/ [R=404,NC,L]

.htaccess rule is not tested, but it gives you an idea.

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