These options apply when Opus implements its own display for the Desktop folder. See Virtual Folders for more information.
You can configure the file display format for Desktop when the native display is enabled using the Folder Formats page, by adding a Path Format for the desktop folder.
The Include additional folders when using Windows Search from the Desktop option at the bottom of the page controls which folders are searched when you use Windows Search (e.g. via the search field in the top right of the Lister) from the Desktop folder. By default, Opus only searches your personal Desktop folder (/desktopdir) and, if configured to appear, the shared desktop folder (/commondesktopdir). If this option is turned on the search will include the profile and shared Desktop folders and also the Documents folder, and potentially others. (It is up to Windows exactly which folders are searched, and you'll see similar from Explorer.)