1. If you have a voice chat running with a friend, it doesn't matter if you are both playing different games to each other.
2. I don't know - I haven't played Civ V online. However, I don't think there is a way to voice chat with others that are just in your multi game unless you add them as friends.
There is however, a group voice chat feature where you can join a chatroom for a group you are in (say you create a Steam group for your clan), the rest of your clan can all join this chatroom (assuming they are members of the steam group) and then click "voice chat" to have a group voice chat. This is similar to ventrilo etc.