I'd exclude both chemical and biological weapons from scope, though for different reasons.
Chemical weapons are mainly terror weapons, and the political simulation isn't really sophisticated enough to handle terror tactics. They do have some situational tactical use, but only on the same level as things like land mines and cluster bombs, and Aurora does not model weapons design doctrine on that level of detail even in the new ground combat model.
Biological weapons, by contrast, fall off the other end of the scope range - like Father Tim said, they get into colony drop territory. While it's reasonable to think people would develop and use them, it's also reasonable to think people would accelerate large asteroids to the kind of speeds usually associated with mass extinction events and throw them at populated planets. Aurora doesn't model that either, and for much the same reason.
Then there is the question of how the game portrays atrocities in general While glassing a planet from orbit is certainly an atrocity, most of Aurora's audience will be culturally conditioned to not really regard terror bombing by air or naval (and by extension orbital) forces as a war crime. All the more mundane horrors of warfare - artificial famines, mass displacement of the population, pogroms, mistreatment of prisoners, insurgency and counterinsurgency tactics, etc. - are not modeled in Aurora, even though many of them are directly strategically relevant at the scale the simulation takes place at. To the extent that this is a deliberate design decision, biological weapons strike me as off the tone Aurora seems to be aiming for.
As cool as it admittedly would be to have one of your xenoarcheology teams find a crashed ship full of eggs and bring some back for the Company's bioweapons division, I think that works better as a ruins event that eats part of your archaeological expedition than it would as a full game feature.