Some of my Safari bookmarks don't appear in Spotlight search results
The ~/Library/Caches/Metadata/Safari/Bookmarks contains bookmarks that get updated by Safari every time you start it. If you look at the date, you will see it only contains the current date.


Spotlight will only show bookmarks that have been updated by Safari in that folder. If for some reason a bookmark is not updated it will not show in Spotlight.


The ~/Library/Safari/Bookmarks.plist does contains bookmarks that are readable in plain text, that file is intended to manage the bookmarks organization.


Spotlight will not search inside this file.


Potential fix:


Remove current bookmarks in ~/Library/Caches/Metadata/Safari since the Safari itself would be unaffected by the removal of the contents and will rebuild it; as I understand it, those files exist to allow Spotlight searches to include bookmarks. 
Close Safari and move the Bookmarks.plist file to Desktop and restart Safari. Now all bookmarks are gone in Safari it self. Move the Bookmarks.plist back where it was and restart Safari and you will have all bookmarks back.