is there a way to hide a specific menu item unless the user is logged in? Right now the link still shows, but it takes them to the membership options page. I'd rather the link just not show.
This is in the development to-do list. In the meantime, you will need to the edit the template for that menu and edit it so it doesn't show items the current user doesn't have access to. WP Admin -> s2Member -> API / Scripting -> Using Advanced Conditionals or Advanced Query Conditionals
It explains how to programmatically show or hide a menu item based on Membership Level (1 through 4) but could be modified to only check whether a user is authenticated or not. Hope this helps!