Short Answer:  Set a canonical url on the pages to the root domain version and noindex the subdomain pages.

What this does is avoid the duplicate content problem.  Generally, those subdomain pages won't rank anyway because the same information is on the "main" site.  You can still build links to those subdomain pages and do a strong internal link structure to help the "main" site rankings.

The only negative to this is that the pages in your subdomain won't rank.  That's not necessarily a bad thing but just know they won't.  But, if the pages are truly duplicate content, they won't rank anyway.

That makes sense.  Thanks.

The answer is "technically" 50,000.

However, the size for sitemap matters too (no bigger than 50MB).

If you have more than these numbers allow for in Google's Guidelines then you break them up and have multiple sitemaps on your site.

Here is Google's Guidelines on Sitemaps:

http://support.google.com/webmasters/bin/answer.py?hl=en&answer=183668