I can’t see how, because the wp_usermeta table contains the metadata about your users. The menu items are stored in the wp_posts table, and the menu options (including the status of the “Automatically add new top-level pages”) is stored in wp_options.
I would definitely recommend that you repair the crashed table, though, because it’s likely having an impact on your WordPress site. See this question and its answers for advice.
Edit
Your posted code looks right to me, and if you’ve assigned the menu properly then it should be working. I’m not sure what the problem might be. Does the menu work properly in a default theme?