Google knows what is what before your visitors do
Google's crawlers have really advanced since there first launch, their crawlers has the ability to detect actual content area, the width of that content as well as the height of the actual content region.
Elements such as headers, footers and sidebars that get repeated on several or all pages are noted by Google and often do not count to the actual page ranks but rather confirm what you have on that page.
HTML5 is great but it's not required
With HTML5 we have many elements like article, header, footer, section, aside, figure and so on that it's believed that this massively helps Google when in fact there's little to none to suggest that a HTML5 site will rank better than a HTML4 site. This is because Google doesn't just code their bots for webmaster that know what there doing. Different content managements and themes work in different ways and Google attempts to cater for all.
Google also knows the importance of being flexible in detecting sidebars on the left, the right navs at the top right, middle and even on the bottom. Google will also be able to adapt to pretty much any design on the menu system after-all the internet would suck if every site was the same.
Some websites use position absolute in there CSS code meaning that even NAV menus that are not above the fold appear in order for search engines but again Google knows what is what regardless where it may be found on the page.
Tug of war Pushing and Pulling
Many frameworks are now starting to use push and pull methods that will change the layout depending what device is being used, but this is generally used for the user not the Search Engines. This is because on mobiles the menu may take up a lot of room while you may want them to dive straight into the content , while on a desktop machine because the resolution is bigger the user will see both the menu and the content.
- Bootstrap for example uses
- Zurb Foundation uses
Experience, Experience, Experience and then Experience
You should always code for your audience and only ensure that you are doing the essentials to improve SEO like ALT tags, Headers and so on. In the rare event that Google dislikes something it may reduce your SEO value slightly but user experience trumps SEO all day long! and the value of visitors that create natural SEO will counteract any minor a hundreds time over. Off Page SEO remains the best way to remain and increase in rankings.