If you pass a false query to Google you can get it to return only the pages that are listed in the main index. Subtract that from the number of pages in a site: query, and you get the number of pages in the supplemental directory.

Example:
site:mysite.com -> Shows the pages in the main and supplemental indices
site:mysite.com -xyz:mysite.com -> Shows the pages in the main index only

In my experience, pages in the supplementals do not harm the rank of pages that are not in the supplementals. However, the pages in the supps are probably pages that you do not want to be there. Typically the best way to get a page out of the supplementals is to get relevant inbound editorial links to those pages. This will signal to Google that these pages are deemed to important to be relegated to the supplemental index.

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The best way to learn anything, is to question everything.