I realize this is a few weeks old, but had a few thoughts.
I typically add scene objects of a shared type to a list and then iterate over a method of their class in update.
So at the end up the enemy class init I would add 'enemies.append(self)' and then in the scene update method add 'for enemy in enemies': enemy.cooldown() or something to that to that effect.
Obviously, you'd have to write a bit more AI methods for the enemy ships, so you'd probably want to subclass them to save space.