If you're running Concrete5.6.1 or higher, you can have your autonav template completely ignore the "Exclude From Nav" attribute by passing true into the $controller->getNavItems() function that appears at the top of most autonav template files:

$navItems = $controller->getNavItems(true);

The primary use case for this is when you have a breadcrumb navigation, because you probably want to show ALL parent pages in the breadcrumb trail even if they're excluded from the primary nav menu. In fact, if you examine the breadcrumb.php custom template that ships with Concrete5 (SITEROOT/concrete/blocks/autonav/templates/breadcrumb.php), you'll see that this is what's happening.

But there might be other use cases where this comes in handy -- for example, if you are creating a tertiary or "sectional" nav menu and you want to show all pages in a limited section of the site, but you still need to use the exclude_nav attribute to hide some pages from the primary nav menu.