As this module is working well with CCK Node reference so it should provide the facility to work with Hierarchical select Node reference module

By making following change, it will work with Hierarchical select Node reference field

file : popups_reference.module
line no : 113

if ($widget_type == 'nodereference_select' || $widget_type == 'nodereference_buttons' || $widget_type == 'nodereference_hs') {

Thanks