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because all the links are pointing to my homepage.
Will it automatically flow through the navigation even if itís done by dropdown menuís?Whether Google sees the links in drop down menus or not depends on the technology used to create drop down menus. If you can see links in the source code, then Google can see them too despite dropdown menu being hidden and only accessible on hover.
The old and new structure of the website is considered good by SEOís and in siloís and in categories.You say that both, the old and the new navigation structure is in silos and categories. If the old navigation structure opened the secondary menu of that category/silo on click, and now you have navigation dropdown menus on hover, then you have significantly changed the structure of your website and (presuming that Google can see dropdown menus), you may now have a situation where every page has links to all subcategories from any option in the main menu. Therefore, your site may not appear as siloed as it was before.
...There are about 100 categories. All incoming links would then be spread evenly over the most importent parts of the site. Would that be a problem? From a user point of view it makes a lot of sense.
IMO, it's a major problem, both for users and for SEO. Too much choice is no choice. It's inherently user-unfriendly. It also makes it essentially impossible to prioritize anything on the site.
I would prefer to rank the subcategories, because they are of much more value for the user. Will this also mean that if I have 20 subcategories they are less likely to rank than when I have only 10 ?