I think it's going to depend on the type Of case if it will affect the wireless charging or not. If it's a thicker case like OtterBox or Defender, it might interfere with it, because Those cases has almost 3 layers of protection. I would imagine Apple tested some of their own OEM cases, which if they're not too thick, I would imagine they would work normally without interfering with the charging. But I think we will see a lot of hands-on tests once the AirPower is closer to launch.
Apple's using the Qi standard, and that standard allows for a distance of up to 5mm between device and charger, so it'd have to be a really thick case before it completely interfered.