The direct links are direct for a reason.
If you don't want them and only want the link to the order (which is already in the email), you can just remove the code displaying the direct links
$statusDownload = explode(',',$config->get('order_status_for_download','confirmed,shipped'));
if(!empty($item->files) && in_array($data->order_status,$statusDownload)){
global $Itemid;
$url_itemid = '';
if(!empty($Itemid)){
$url_itemid='&Itemid='.$Itemid;
}
echo '<p>';
foreach($item->files as $file){
$fileName = empty($file->file_name) ? $file->file_path : $file->file_name;
echo '<a href="'.hikashop_frontendLink('index.php?option=com_hikashop&ctrl=order&task=download&file_id='.$file->file_id.'&order_id='.$data->order_id.$url_itemid).'">'.$fileName.'</a><br/>';
}
echo '</p>';
}
in the emails via the menu System>Emails (business edition).