I’m wondering what happens if I upload the same file to more than one notebook. Does each copy count separately against quota or are they de-duplicated on the server?
No, we don’t de-duplicate for the quota. If you upload the same file twice, we count it twice.
But you can import the same file many times. You could upload a bunch of files to one notebook, with a named cell for each file (or an array of all the files), and then import the files to your other notebooks.
Forking a notebook with files also doesn’t count against your quota.