Clearly you are correct - it is only guns that rely on remote power control that would be affected by engineering failure and you should adopt a special rule in any scenarios involving ships with guns 5.1" and larger that are not normally power operated. Hand cranked guns such as Graf Spee's single 5.9"s and French DDs' 'semi-turret' 5.5"s, for example, would be largely unaffected by engineering hits and would fall into this category (but note that Prince of Wales' 5.25" guns had back-up manual operation but could not be effectively trained by hand after she was struck by Japanese torpedoes, due to the list of the ship, so it's not entirely straighforward).
Note that power failure also means reversion to local fire control, so that penalty would apply to hand operated guns normally relying on following the central gun director's (power operated) pointer.
This is yet another example of GQ3's oversimplification of complex real world issues - you can accept it for speed of play, or if you don't like it, adopt your own special rules as part of the scenario you are playing. But the answer is not in adding more complexity to the main GQ3 rules - these need to be kept as simple as possible. Lay persons and casual onlookers already find them impossibly complex compared, say, with Monopoly.