You can disable the display of references from the Preferences > CodeMix > Settings > User Settings page.
Select ‘Code Mining’ from the dropdown and set the referencesCodeLens.enabled to false according to the type of the file. Please see the attached screenshot for your reference.
Can you try to change values for the same properties but in Workspace Settings instead (CodeMix -> Workspace Settings)?
In general, a value customized in Workspace Settings overrides the one from User Settings. To simplify and remove possible confusion, we have decided to drop a direct support for User Settings in CodeMix, starting from today (we have just pushed an update).
Application Development Manager