Users have the ability to hide themselves from the Directory if the 'Allow users to remove their name from the online directory' check box is checked under 'Profile Publish Access.'
To stop Users from hiding themselves:
- Navigate to Core> Security> Profile Access> Profile Publish Access
- Click 'Edit' at the top right
- Uncheck the box next to 'Allow users to remove their name from the online directory'
- Click 'Save'
Users will now be unable to hide their name from the Directory.