I would go for a single physical library. Otherwise it's a pain to search for something you may not remember every detail about, or to perform any library-wide operations.
OTOH, if you're sure you don't ever want to do the same things with, say, fiction books and technical PDFs, you could keep them separately. It all comes down to personal preferences.
There is a somewhat worse performance with a huge library vs a smaller one, but for me personally the convenience of using a single library is worth it. YMMV.
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