Whether you keep separate libraries each in thir own folde is up to you. Note that if you do decide to split your library make sure you use the Calibre facilities fr copying books between libraries if you want metadata to stay intact.
I prefer to use saved searches in conjunction with appropriate tags to keep 'virtual libraries' within one physical library. You can apply a saved search as a 'restriction' to operate on a sub-set of the books and treat that subset as if it were a library of it's own.
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