Best answer by Arjan Sollie
The set of prefilters which are displayed within a subject variant, should be added on the base configuration of this subject. If you would like to hide a specific prefilter in your 'standard' subject, you should also create a variant which you will use as the standard display of you subject.
It is also possible to hide a prefilter on the standard display and enable this prefilter within a variant. However this will lead to unwanted issues, regarding the availability of this prefilter within this variant and therefor is not advised.