This just happened to me. Then I've uninstalled the latest two packages that I had installed and the Preferences menu became available again. The two packages were "Advanced CSV" and "CSV". Sublime Text 3 version 3176, OS X High Sierra 10.13.4 (17E202).
And then I installed these packages again, but the menu still works. At some point, some submenus were greyed out (while I was editing user settings for the package), but then they also became available again.