The system HP condition system if you go under X%HP is mentioned in the build mode view, but the modifiers themselves are not applied on the systems.
10 000 power regen/sec at 100% HP is still 10 000 power regen/sec at 15% HP. The game says it should be 60% at that point so that should be 6 000 power regen/sec. As far as I can see this is also the case for thrust although that's harder to test.
Both the gui numbers and the ones used (tested out with a cloaker) are not changed.