The solution works only for the Pro plugin version.
To exclude from search products from certain categories, go to WooCommerce -> FiboSearch and choose the “Search config” tab. At the bottom of the config page, you’ll see the following section:
Set Filtering mode to “Exclude” and then set Filters to the categories you want to exclude from search. You can also exclude products with given tags.
Save you changes and rebuild the index. From now on, products from selected categories won’t appear in the search bar.