The second Advanced Setting when creating a Subject, require completion of Subject, is enabled by default. If you switch to reference only, then completion will not be required for users assigned to the Subject.
Users can still view the Subject, but no completions or progress will be tracked. Since completion is not required for reference Subjects, these Subjects are not included in Reports.
If you have "reference only" enabled in Subject Settings, then the rest of the settings are hidden (as shown in the screenshot below) since they can't be combined with a reference only Subject.
Reference Subjects will also have a "reference" tag on your Subjects page like shown below, so you know which Subjects are reference only.
Lastly, you can filter My Desk by reference material.