I'd disable it so you can re-use the island coding later. The system itself was designed so that the islands cannot be removed as some host configurations will not allow you to automatically re-create flat files that are on the system without proper configured permissions (CHMOD); so I'd leave them and modify them later if you need to use a custom island. Islands that are not in use are only ever displayed on the Custom Islands and Portal Settings pages in the Control Panel.
This feature has not had any attention in any recent releases, you can watch Changelogs to see if it has been addressed versus posting to ask; all Changelogs are available as they're posted in the
Changelog Discussions forum
