What do you mean by “everything not being used”?
Unless broken, the server data directory should only contain stuff that’s used.
You can however remove options you don’t want to use, e.g. disabling the option to create preview thumbs in each library’s advanced preferences (this can use quite an amount of storage). There’s also an option to remove previously generated preview thumbs.
Edit: another option could be to move the server’s data directory to another (bigger) drive – e.g. if you don’t want to miss out on the storage-hungry options.
