I do so by Javascript, just so it doesn't look so crowded. But, this is rather a touch-up and doesn't hold up if security concerns are prevalent. In /dokuwiki/conf/userscript.js
following code:
jQuery( "li.closed > div.li > a.idx_dir[href$='events']" ).parent().parent().remove();
jQuery( "li.closed > div.li > a.idx_dir[href$='wiki']" ).parent().parent().remove();
jQuery( "li.closed > div.li > a.idx_dir[href$='user']" ).parent().parent().remove();
jQuery( "li.closed > div.li > a.idx_dir[href$='scrapbook']" ).parent().parent().remove();