Hi,
HikaShop is compatible with Sh404SEF. However, you found the only link which is missing the itemid parameter. Because of that sh404sef screws the link.
If you use the latest version of HikaShop, edit the file "show_block_product_files" via the menu Display->Views and change the code:
$fileHtml = '<a class="hikashop_product_file_link" href="' . hikashop_completeLink('product&task=download&file_id=' . $file->file_id) . '">' . $file->file_name . '</a><br/>';
to:
global $Itemid;
$url_itemid='';
if(!empty($Itemid)){
$url_itemid='&Itemid='.$Itemid;
}
$fileHtml = '<a class="hikashop_product_file_link" href="' . hikashop_completeLink('product&task=download&file_id=' . $file->file_id.$url_itemid) . '">' . $file->file_name . '</a><br/>';
and that will avoid that sh404SEF break the link.