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Most changes to metadata in calibre are only written to metadata.db.
When books are saved to device or to a folder outside calibre, the metadata in the book is written to the book, to the extent that the file format has support for the metadata. Polish, conversions and some plugins to update the books also cause metadata to be written to the books.
You can easily confirm this by changing some metadata for a book (other than title and authors) and check that the book has not been changed.
There are numerous warnings about not looking up the skirts of calibre, including sticky threads. You are NOT supposed to directly access books inside the calibre library, unless you know what you are doing and why. If you don't know about the "lazy update" of metadata then you obviously shouldn't peek inside the calibre library file structure.
The reason for the lazy updates is (I assume) that it makes calibre MUCH faster, both when it comes to searches based on metadata and when it comes to changing the metadata.
But it also makes it possible to corrupt the calibre library if you makes changes to the books stored in the calibre library, without using calibre.
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