A number of people worry about this - but there should be no worry, because as you said, you can't have a hover-style menu without having some content not visible when the page loads. The fact is, all the content IS visible in your source code, so it's not hidden to search engines.
The only time you can get into trouble is when there is no natural user action that makes the content visible. Then you are serving content to Google that you are not showing to regular visitors.
I've been using a show/hide menu system for many years on many sites and have never seen a problem.