indyank - 6:38 am on Feb 17, 2013 (gmt 0)
@1script, You haven't mentioned how how you are handling sub pages of these category pages.
But here is my take.
Adding noindex to category pages don't mean they block flow of PR thro. them. They can still pass on PR. You are confusing noindex with nofollow. It is nofollow meta tag that essentially prevents flow of PR. If you just added the noindex meta tag, then PR can continue to flow thro. those category pages. The deafult is "follow".
But whether to noindex or not is your own take. I would suggest if the category pages have some great collection of topic relevant products/articles, you can allow them to index. But if I remember right,google somewhere suggested not to get tag pages or search result pages indexed. Do you find these category pages different from those tag or search result pages? if yes, allow them to index.
Coming to sitemaps, it doesn't really matter if you have noindex pages on them. Yes i know that one wp seo plugin spread that myth but in my exp., it is no harm to include them or leave them alone.