If you install MATE Desktop, you'll see Kali Linux Menu item is missing and it's been replaced with Other item which is just a collection of all PenTest application shortcuts.
Also if you look into System>Preferences> there's two Main Menu icons. One of them is mozo and the other one is alacarte. Alacarte got Kali Linux item, mozo is however missing it.
How to get back Kali Linux item in MATE Main Menu?
p.s. Deleting /root/.config/menus or /root/.local/share/applications doesn't solve it. Neither does reinstalling kali-menu.