At https://confluence.atlassian.com/display/FISHEYE/Repository+options there's a note saying:
Some changes will require the repository to be restarted, while others will require the repository to be re-indexed. FishEye will advise you if this is the case when you make the change. You can restart a repository from the 'Repositories' screen, by using the Restart function for the desired repository.
However, after setting Inlcude/Exclude Paths for Defaults and saving the settings the user doesn't receive a warn about restarting/re-indexing the repositories, so the changes aren't applied for existing repositories unless the user knows the repository needs to be restarted or re-indexed.
I also verified it doesn't ask for a restart on the repositories when setting a Hidden Directory.