The +1 is part of the shield's AC bonus for this purpose
Unlike in previous editions of D&D, 5e has very simplified shield rules:
Wielding a shield increases your Armor Class by 2.
Naturally, some shields are special; the +1 shield mentioned increases your AC by 3 instead. However, if "special" shields that give different AC bonuses aren't intended to affect the benefit of Shield Master, then Shield Master could simply be worded as "add 2" rather than "add your shield's AC bonus". Since the wording of the feat implies that some shields give a different bonus, and magic shields are the most common reason I know of that a shield would give a different bonus, I conclude that the different bonus from a magic shield is intended to apply.