I usually get two or three morality check events every game, when colonizing planets. I colonize from 5 to 12 planets in my games, using Large map, common stars, uncommon habitable. So it may have something to do with your map settings, or how aggressively you pursue the colony rush. The more planets you colonize, the better the chances of triggering one of those "do we kill the intelligent worms" type events.
I also just got the "zombie army" research event/morals check in my current game. I'm playing with some race points added to the Lucky attribute. Maybe that helps trigger events like this? Anyway, they're in the game, they just don't happen all that often.
