I just wrote an article about this lately. Though the article is specific to a js menu in Wordpress, the reasons for not using this type of menu are pertinent to anyone using or considering using javascript menus.
http://kickasswebdesign.com/wordpres...ibility-no-no/
Google Webmaster Guidelines has this to say: "While Googlebot is great at understanding the structure of HTML links, it can have difficulty finding its way around sites which use JavaScript for navigation. We’re working on doing a better job of understanding JavaScript, but your best bet for creating a site that’s crawlable by Google and other search engines is to provide HTML links to your content."
Why can you not use php to include the menu? It renders like html and you can include the file.