I am printing dir of each of my disks and I just removed Plex which was installed as an add in instead of a docker. I rebooted after uninstalling it but I still have a Plex share and plex folders on all my disks with tons of subdirectories I'd love to delete. What's the best way to remove them? Will deleting the share get rid of them or do I have to delete them from each disk?

You should be able to delete the files and subfolders from the user share and that will delete them from all of the disks. Then you can delete the empty share from the webUI.