I use CyanogenMod, and denying wake locks doesn't solve this problem. An application can register to receive any number of events that will wake it despite a lack of wake locks, like geofences, alarms, push notifications, waiting for another app to wake the device, etc.

It's the same reason that denying the permission to automatically run on boot is basically useless from a privacy perspective -- the application will just automatically run when some other event happens.