If you kill all the hybrids as they appear, they never mature into the advanced forms, and the advanced hybrids plot won't have any effect.
Advanced hybrids lets them build higher mark modules at higher maturity levels, enables the super hybrid (which is scarier than a usual hybrid), and enables various intensity-gated interactions with the Dyson Sphere. May also allow builder-hybrids (one of the maturation routes) to build more stuff, unsure, that was going to be a thing but I'm not sure it was ever added, or if builder hybrids are even a thing anymore.
There used to be a 'defensive hybrids are mobilizing' dirty trick that could happen when advanced hybrids were on, but that was disabled due to initially appearing to do nothing, then to being far too lethal.
One very important note about the Hybrid Hives plot: The intensity controls how many Hive Spawners are seeded
per eligible planet. The total number of eligible planets is strongly dependent on map size, and somewhat dependent on the map style. The smaller the map, and the more planets near your homeworld, the more you should bump the intensity. Mantis issue for changing that located here:
https://arcengames.com/mantisbt/view.php?id=18807
