I didn't change anything in my shortcuts. If I try to use 'Ctrl++' or 'Ctrl+=' to zoom in I get:

The key sequence 'Ctrl+=' is ambiguous. Use 'Configure Shortcuts'
from the 'Settings' menu to solve the ambiguity.
No action will be triggered.

The key sequence 'Ctrl++' is ambiguous. Use 'Configure Shortcuts'
from the 'Settings' menu to solve the ambiguity.
No action will be triggered.

Zooming out with 'Ctrl+-' works fine.

If I try to reconfigure the zoom in shortcut i get:

The "Ctrl+=" shortcut is ambiguous with the following shortcut.
Do you want to assign an empty shortcut to this action?
Shortcut 'Ctrl+=' for action 'Zoom In'

And the problem persists after I defined Ctrl+= and Ctrl++ as custom shortcuts.

I found the problem: Okular can't handle the third modifier key of my keyboard layout (de neo 2)
To be more precise: Somehow 'Ctrl' plus 'B' and 'Ctrl' plus 'Mod3' plus 'B' are falsely detected as ambiguous.

The shortcuts themselves work, if I remove one of them, if I remove 'Add bookmark' then 'Zoom in' works with 'Ctrl' plus 'Mod3' plus 'B' but 'Zoom in' does not work with 'Ctrl' plus 'B' – so its only the "ambiguity detector" that can't handle the modifier key and there is no real ambiguity.

Could this somehow be related to bug 343665?
There seems to be some confusion over whether it is actually resolved, can someone clarify?
Can someone advise if this should be reported as a bug?

I reproduced it today on a fresh Kubuntu 16.04 install.