If Google can’t see your navigation clearly then it struggles to understand your site structure and it might not even index a lot of your pages: because it can’t find them!
There are ways around this, such as building a sitemap.xml file to give Google a roadmap of your site (something we recommend for all websites) and also creating a well structured human readable sitemap page, again to help Google understand your site structure.
But how can you tell if you have a problem? Use a tool such as the www.seo-browser.com. Type in your web address and then look at what it shows you. It will give you a good idea of what Google will see. Below is what our site looks like using this tool; note how the navigation is very obvious. Remember, if you can’t see any navigation links then neither can Google!