This is an old known problem that tends to pop up on non-US keyboard layouts but can also affect things like Cmd-+ for zooming on a US keyboard (since + is Shift-= on a US keyboard.)
One related Trac ticket: #2499 ([Keymap] shortcuts don't work with some keymaps) – Haiku
The reason for this is shortcuts can include Shift but the system does not consider Cmd-+ and Cmd-Shift-= equivalent (on a US layout) even though it should.
This becomes tricky because it means the shortcut system needs to know the keyboard layout and would need to assign “synonyms” for the shortcuts that need to be shifted. Also this should probably not apply to letters because Cmd-[letter] and Cmd-Shift-[letter] might be useful as separate shortcuts. Also what happens if different actions map to the same “synonym”? Research should be done on other systems to see how they handle it as well.
I think either way the above needs to be fixed but there has also been discussion in the past about making shortcuts configurable. At the moment that would need to be done inside each application, which is painful. Ideally Haiku provides some sort of system for applications to register their “actions” with default shortcuts that could be changed in a system Preference app (in this case obviously it would be the Shortcuts app which would need to be adjusted.) This system would also have a bunch of common default actions already like Cut, Copy, Paste, Open, Save, Undo, Redo, etc.
But adding something like that is a new Haiku feature and would require a developer with interest and also need to be supported enough by other developers to be reviewed and merged. Updating all included Haiku applications to use this new system might also be a lot of work, unless it can be done in a clever way which requires minimal application code changes. Which may be possible but we would not know until someone tried. But it would likely be a very useful change.