Thats your problem then.
You are correct khotkeys is deprecated. Even if you previously used it for shortcuts, you would need to remove it and apply them again using kglobalaccel.
I dont know how you are missing kglobalaccel, as its part of plasma.
sudo pacman -Rns khotkeys
sudo pacman -Syu plasma-desktop
As mentioned, kglobalaccel is a dependency of plasma-desktop.
Your shortcuts should be configurable through System Settings as usual.
And/or directly by kglobalaccel.
PS
Your missing core packages makes me wonder about the general integrity of your system.
Have you accidentally removed things?
Performed a partial-upgrade?