It all depends on how Joomla is used in your site. If you are using Joomla's polls, comments, ratings, or any other extension, then it would make sense to integrate the user logins/database.
If you are using Joomla just as a CMS and you and/or your staff are the only users adding/editing Joomla content, then you don't need the user login integration. Which in my experience is usually a pain.
We started with full integration, and eventually turned it off and now only the skin is integrated.
Recently we switched the home page to vbAdvanced (to provide member logins, threads, etc), and some of the content pages are in Joomla.
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