Hi, the problème is that when you delete the menu item via joomla it's not really deleted but the published state go from 1 or 0 to -2 and is not displaye don the menus listing of joomla. So we will do the same.
Just edit the file administrator/components/com_hikashop/views/menus/view.html.php near line 160 and just before the line
, please add the code
$filters[] = 'published>-2';
to fix the problem. It fixed the notice on our end and we have the same behavior as joomla which is to not display menu items which are trashed but not deleted.