Different databases make sense if you have completely different kind of data sets. For example: If I wanted to create a book database that also stores authors and publishing houses, I would create 3 separate databases and link the authors and publishers from the book database.
Categories make sense if the data is similar, but a structure makes sense for the user and/or if fields need to vary. That book database might have a field for number of book pages, that gets turned off just for the e-book category for example.
Lastly, it can also make sense to not use categories at all when you want to use fields as filters which can act on the entire database, not just categories.