In my experience, there are two very big users of space in the limited "application data" section of the N9's storage.

One is the mail storage. The only way of cleaning that space would be to delete your accounts and recreating them, to get rid of all downloaded message bodies, attachments and images. Unfortunately, I don't think you can delete the contents of the folder where the mailboxes are kept without losing the mail account configurations...

But it's probably easier to attack the folder /home/user/.thumbnails, which is usually hidden. It contains thumbnails in various sizes for different places in the UI, and by far the biggest is the .thumbnails/grid folder, which has the thumbnails of photos and of social media posts. There's so much of them that you can't just rm *.jpeg, you should use a command based on find, which I can never remember how to do or even if it works on the special shell used by the N9, so my (ugly) workaround is:
Be careful with the rm command, it's very dangerous.

This is also a great way of dealing with the issue where the mmcblk0p3 partition runs out of inodes (as reported by df -i )