Currently in Missions in Chicago, all Awakened players are suffering dice pool penalties when doing runs in the CZ because of the native background count. The highest I have see the BC in the CZ is 10. So, in a way, Awakened are boned. Additionally, Technomancers and Deckers are boned in the CZ because of the native noise penalties of the legacy grid (Noise 2) and some of the places were you have to go to, which may or may not include underground where you will suffer -5 or greater.
Keep in mind, this is only for Chicago when playing SRMs. The CMPs will take you somewhere else in the 6th World.
Players that rely on chrome or tech usually convert Karma to Cash (Working for the Man, 5k for 10,000y) and use left over Karma built up over time for improving skills or stats. And it is the opposite for Magic users (Working for the People, 10,000y for 5k). And you can do this once after every mission.