My last response on this: my whale ship(s) have been able to farm the most difficult missions for some time - so this isn't said with no experience in gearing/creating a viable whale ship.
Given the choice between 1k def and 1k atk for my ship, I'd take the 1k atk. As you point out, atk gets a 40% modifier after the chance panel. If you have the correct slash/pierce/hit/magic/nuetral type ship, you get a 50% bonus to atk. So a choice between 1k in def versus a 1k in atk should be thought of as 1k def versus 1k * 1.5 *1.4 = 2.1k atk. I'd take 2.1k in atk stats over 1k in defense stat.
Having your whaleship survive the mission is done in two ways: a) surviving long enough and b) killing the ancient pest faster. Since bonuses apply to atk and not defense, in a 1 for 1 stat debate - take the stat that gives bonuses.