goodroi - 6:52 pm on Jan 2, 2013 (gmt 0)
I regularly use htaccess to block Google from accessing certain pages and I have not noticed any issues. I don't recall using it to block 100,000s of pages on one site.
Google tends to crawl pages with more traffic and backlinks going to them. If you want Google to pay more attention to a page, see what you can do to boost traffic and/or backlinks.