Anything that affects a Stat or Ability SHOULD be working, some ofthe more specific ones (city stationing bonuses, per-turn global resource bonuses from sovereigns, etc) or boosts on things not yet implemented (army morale) are not. I'm about to go through the data and round up the lacking bonuses and penalties.
Hmm... if that's the case, I don't understand how those work then technically. Is it different from the ability bonus for civs then?