Will using a thermal hardener and a kinetic hardener at the same time cause one of them to be penalized?
What if I use a thermal hardener, thermal resistance plating, and thermal energized plating?
How is the penalty calculated?
The stacking penalty applies to the bonus, not to the module.
If you have a thermal hardener and an EM hardener fitted, both would provide the full resist bonus. If you add omni-resist plating, its thermal and EM bonuses would be reduced because of the stacking penalty, but its explosive and kinetic bonuses would not.
The precise formula is somewhat complicated, but it can be summarized as:
The order you fit the modules doesn't matter; the one with the largest bonus will always be considered "first".
Some modules (notably Damage Control Units) are exempt from stacking penalties.