Yes quite a few modifiers, when they say for example -20% damage, it really means the incoming damage is increased by 20%, which really means you get +25% to your effective hit points (EHP) i.e. your flux bar. However, you still dissipate your flux at the normal rate, so it's quite often better to take the damage reduction over more caps if it's close, since you'll dissipate the flux more quickly that way. For example if the incoming damage is 200, if you chose more caps then you have to dissipate 200 flux, but if you chose Hardened Shields (-20% damage) you only have to dissipate 160 flux.
With armor/hull it becomes more complicated, since reducing the incoming damage also reduces its hit strength. For example, Impact Mitigation says -25% armor damage taken. This does not mean "if the shot would've done 100 damage to armor, it now does 75 damage instead". Instead, it means the shot is calculated as coming in with 75 damage, which also means its hit strength is now 75 instead of 100 instead. That latter part also decreases the damage further. For a good number of armor-to-hit strength ratios, it'll actually reduce the damage by around 40% -- so if the shot would've done 100 damage to armor, it now does 60 instead. So those damage reductions are actually significantly stronger when you consider the armor mechanics.