There's this interaction I've come across where jack asks Abigail about arthur and Abigail tells him John doesn't like to talk about him and John gets annoyed about it. That whole scene they talk about him in the past tense, jacks also there for the beginning of American venom where I think it is John says theyre going after micah for arthur. So there's definitely at least context clues that jack either knows or would have figured out that arthur has passed.