I'd also really like to know this. I had the same thing happen-- I attacked a few ships, didn't notice any negative reputation with their owners (or with anyone, when I attacked unaffiliated merchants). I assumed that ships having faction affiliations meant that attacking them would hurt you with their owner, but it hasn't seemed that way so far? I'd like to make an informed decision about whether or not I'm secretly making everyone in the Deadfire hate me in some way that isn't represented on the faction disposition chart before I continue pirating on everyone.
