I've succeeded in persuading them about the ship being full of monsters.

They fled, encountered the githyanki captors and FOUGHT TO THE DEATH.
Only Gimblebock survived and couldn't attack the gith because she was still in the cage.

Isn't the deception option actually true? As the ship was invading and capturing Baldur's Gate and its citizens. Also I can't find any reason not to attack the bandits within the ruins/bedchambers, has anyone found a reason not to fight them?

To get good amount of xp and gear from them, use whatever dialogue option you want to convince them to not attack you. Then as they run away, attack of them and start the fight. That way you get the xp from convincing them plus the gear and xp from killing them.