Navigation links count, but they play a different role than contextual links and cannot replace them. The cleanest way to see it is to split internal linking into two jobs: structure and discovery on one side, topical relevance on the other. Navigation and boilerplate links handle the first. Contextual in-content links handle the second. A strategy that leans on one and ignores the other is missing half the work.
Navigation links do real work. Because they sit sitewide in menus, footers, and headers, they pass equity and give crawlers consistent, reliable paths to your main sections. They establish the skeleton of the site, tell search engines which pages are central, and make sure key hubs stay shallow and easy to reach. Dismissing them entirely is a mistake, because without them important pages would lose their most stable route to discovery and a share of the equity that flows through the template.
What navigation links cannot do is carry topical relevance, and that is where contextual links earn their weight. A menu link appears on every page regardless of subject, so it is contextless: it says nothing about how the linked page relates to the specific content around it. Search engines weight in-content links more heavily for relevance precisely because their placement and surrounding text signal a genuine topical connection. So treating a navigation link as equivalent to a contextual one overstates what the sitewide link communicates. Nav links anchor structure and crawling; contextual links tell search engines what a page is about and which other pages share that topic.
Build the strategy on both roles deliberately. Use navigation to keep your hubs and core sections shallow, consistent, and reachable, and rely on contextual links inside your content to connect topically related pages and pass relevance where it matters. Count your nav links toward structure and discovery, then add contextual links wherever a genuine topical connection exists, and let each layer do the job it is actually suited for.