One of the things I love about calibre and using search on both calibre and my eInk devices is not having to waste time maintaining a complex directory structure to allow easily finding books. Hmmm... want to locate all books with Al Robertson as a co-author? Easy-peasy with search. Using a directory structure? A massive PITA.
As for using calibre with Dropbox, if you are very careful to only use one computer at a time to access your library and are very, very lucky, you may be able to use Dropbox to store your library. Unfortunately, there are just too many message on Mobileread starting with words to the effect: "I've had my library in Dropbox/OneDrive/iDrive/Amazon Cloud/Box/whatever for years and suddenly I can't access my library/I'm getting errors accessing my library/hundreds of books in my library have gone missing/whatever other errors you care to think of. Most of the time the response is to point the user at
I am getting errors with my calibre library on a networked drive/NAS?.
For me, local storage for libraries and a one way sync to my various backups works just fine.