I don't think an official response ever got posted for this question, so I'm posting one:
Multiple sources of % modifiers (buff hammer + charged rounds, buff hammer + kerosene, etc) are additive. That is, the final value, whether we're talking about engine thrust or shot damage or whatever, is
(base value) * ( 1 + (modifier1 + modifier2 + ...) )
This applies equally to negative modifiers; Impact Bumpers is (I think) -60% thrust, and buff hammer gives +25% thrust, so if both are active you have 65% (1 - 0.35) of your engine's normal thrust.