While you add this features (or “re-add” them, because they were in GeoTheme), I’ve done the job loading this JavaScript on header:
<script language="javascript" type="text/javascript">
jQuery(window).load(function(){
jQuery(".geodir_map_v3_home_map_2_map_category .main_list > li:first-child > input").trigger( "click" );
});
</script>
This works for me because the category that has got subcategories is the first one on the list and the class name of my map is “geodir_map_v3_home_map_2_map_category”. Other configurations may need some tweaks, but anyone can improve this code as needed ;).