Adding a shield generator, armor, or any module has no effect on ships with an armor, shield, or hull integrity bonuses. The % boost doesn’t show up in the summary at the bottom of the screen. For example, I’d expect putting a single Ultraheavy Armor (126 absorption) on a Stingray Cruiser (10% bonus) would give 126 * 1.1 = 138.6 average armor, but it only gives 126.
When adding power or engine modules to a hull with a % boost to power output or engine speed, the ship design screen values change exactly as expected.
I thought it might be possible that the values are applied during battles and just don’t show up on the ship design screen. I wasn’t sure how to test that, though.