5-90,
"I do know that oxide layers are naturally-occurring in metals, but are they always desirable? That's the question here... "
From what I've read and understand, if copper is cleaned with ammonium hydroxide this cleaned area is prevented from forming protective oxide layers. So continued exposure of this unprotected area to corrosive chemicals, causes the copper grain boundaries to start to corrode, i.e. intergranular stress corrosion takes place. As the grain boundaries continue to disintegrate/weaken, the copper eventually cracks and breaks apart. So, in my view, the oxide layers would always be desirable because they prevent breakage at the grain boundaries.
Best regards,
CJR