Calibre use the title and author to create the folder where the book is stored, in the internal storage used by Calibre. Since there really is no reason for this information to ever change, once it is specified correctly, this is very reasonable.
Just make sure to use the correct title and author when you add a book, then that book will never have to be moved internally between folders in the internal directory structure of the Calibre library. And all other changes to metadata will be almost instantaneous, since they don't actually change or move the book.
You might also want to check your computer and the filesystem. The times you mention seems excessive, even considering the sizes of the books. Or do you store your Calibre library on a slow external device of some sort?
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