Integration with the WP3 menu system is coming in the next update (probably next week).
Currently, if you have a parent page in your menu, and you restrict one of it’s children, the restricted child page will be still be listed in the menu (although the page itself will not be accessible to anyone without privileges). Ensuring this feature is “in” and working correctly is definitely a top priority.
I should clarify that the reason this didn’t make the initial release is due to the fact that WP 3.0 does not yet have the appropriate hooks to filter menu items the ‘ideal’ way. Currently, to block pages from rendering in the menu you have to provide WP with a list of exemptions (the ids of pages you want to leave out of the menu)… and performing this kind of check on every visit to any page with a menu could easily be EXTREMELY costly in terms of performance (you could easily end up checking the current user against every page in the entire database on every single page view… ouch). To get this feature working (and to also improve speed and minimize overhead) we’re looking at possibly caching permissions restrictions on a user-specific basis… which would require changing the way a lot of the existing security works.
In the mean time, I plan on submitting a couple new hook requests to hopefully make the next WordPress update.