Having a proper server available is even more reason to use a proper fileformat. The client doesn't care what the server handles and the server doesn't need to send raw datastructures directly from the storage.

Actually, fixing the fileformat-mess should be very simple. Just change the file-load/save-functions. Use a folder-structure with every cell being a seperate file. Or switch to XML. Or make a generic interface and allow to save in whatever the people want. Saving notebooks in Mongodb or some SQL-Database seems like a good goal for dedicated services.