I think of “Clean up Library” as a thing that should be used with a goal in mind. It’s not designed to be a form of periodic maintenance. I don’t think I’ve ever used it on my “real life” collection.
Sometimes it’s used to help Roon “forget” about bad edits you’ve made, especially if you’ve gotten some content into a hopeless state using “merge albums” or “identify album”. You can move the files outside of Roon’s view, use “clean up” to tell Roon forget about those edits, then move them back and start from a clean state with those files.
It’s also useful to clean things up after accidentally allowing Roon to see multiple copies of your library at the same time. This sometimes happens by accident when migrating from iTunes to directory storage, when migrating your install between machines, when installing a new NAS, etc.