To hide categories from the autocomplete section, you can set the number to 0 to disable it. (Stores > Algolia Search > Autocomplete Menu)
Alternatively, you can add a filter to all your front end queries that exclude the relevant categories. You can add a filter to your search widget by following this guide for customizing your front end in Magento. You can do this with the searchFunction in your instantSearch widget, adding filters or facetFilters using NOT or "-" respectively. If you choose this option, ensure that you use the provided hooks and Magento best practices.
Lastly, you can prevent them from being indexed altogether. If you choose to not index them, you can use the guide here and note what products are indexed, and toggle those settings to prevent them from being indexed. Otherwise, you can deactivate the category by setting (Catalog>Categories) Include in Menu to No, and making sure that Show categories that are not included in the navigation menu is also set to No (Stores > Algolia Search > Categories).