Yes, it’s one of possible problems. Though we can treat a renamed item as a combination of deletion and creation of a new item, so it’s OK for shortcut to disappear :)
Another big problem with hashing menu items names will appear if a plugin supports different languages in its interface. In such case, different language will lead to completely different item names. Though, in case of menu items added by user it should not be a problem - since these items are added by user who fully controls the item names. But the problem with renaming of a menu item (after a shortcut has already been asdigned) still remanis.
Maybe it would be worth to add some kind of Menu Items Manager to Notepad++'s plugin interface to deal with custom menu items created and modified by plugins.