Hi,
You're right on the IS NOT NULL, and I've removed it from the three queries in hikashopMenusClass, plus the two other places which had the same copy (the menu item lookup in the helper and the Smart Search plugin). It will be in the next version.
A bit of history, since it explains the shape: that filter was added in 2014 next to a LEFT JOIN, where it was the way to drop a menu item pointing at a menu type which no longer exists. The join was changed to INNER the same day and the test has done nothing since.
The join itself I'm keeping, as that is what now does the filtering the NULL test used to do: an INNER JOIN on #__menu_types excludes the menu items whose menutype has no row there. That shouldn't happen on a healthy site, but we do see databases where a menu was removed and its items stayed behind, and picking one of those for an Itemid gives a link which 404s.