Any equipment changes to an aircraft is usually controlled by engineering. A document stating each step (usually with sign-offs) is needed for completion of modifications.
Wires should never be left open. Termination with crimp on caps or heat shrink are normally used.
If an alternative APU model is to be implemented, necessitating the removal of equipments associated with the currently installed APU and the installation of components specific to the new model, is it required to terminate or cap the existing wiring from the previous system?
The provided print shows the wiring and plug are already installed.
The wires have identifying numbers along with the plug having a equipment list number.
All of that "has" been installed unless a engineering order or documented change has been accomplished.