rotating content

I'm working on a site: http://www.articleinsider.com.

It looks like the person who originally set up the site chose to use article Taxonomy rather than Menus to organize the site, which contains 50,000+ articles.

Here are the issues for discussion:

1) What are the benefits of a taxonomy organization over a menu organization?

2) It seems that on some category level pages, there are articles (which rotate as you refresh the page) - while on other category level pages, there are simply links to articles or subcategory pages.