When analyzing our shop system, all SEO tools complain unanimously that there are too many internal links. We have a main menu bar integrated into all shop pages, containing links to our about 900 categories and subcategories in a tree-like view.
Now, adding resonable text to the categories and linking to it's subcategories seems like a waste, as it is only one link in about a thousand, making the process a bit ridiculous.
Is there a way to tell search engines something like "This is only a menu, don't listen to all the links it contains" via HTML? We'd like to keep the menu as a navigation option for users used to it and not remove it just because the SEO analytics complain about it - usability over SEO, if you will.
How is this solved in general, without compromising the navigation option?