I published a small patch on github for omeka (https://github.com/omeka/omeka-s/pull/1423) to get only the used terms. It’s available in module Next too. When installed, you just have to add the option "used_terms" => true,to the select (in the theme) or used=1 in an api query. An parameter is added in the site settings too to be applied by default in the advanced search page.
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