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.