As mentioned in Chapter 5. Advanced Editing Tools,
To place comment markers, use the Tools → Comment menu item or the related keyboard shortcut sequence, the default is Ctrl+D.
To remove comment markers, use the Tools → Uncomment menu item or the related keyboard shortcut, the default is Ctrl+Shift+D.
The shortcut did work. But I can’t find them in the tools menu. Instead, I can find them in configure toolbar. So where are they?
Unfortunately, not everything that kate does is available in the menu system - which is understandable as it does so many things and the menu system is already quite huge (larger than any other KDE application, maybe with the exception of KDevelop).
But everything is available from the command template (ALT+/) so there is at least that.