The short answer is yes, they should still be listed. The default setup will have them see the conversation when a reply comes in. The "ignore" option is designed mostly for abusive type conversations where the action is explicitly silent (and should be).
So my question is how do other members know when a member is active or not? That is confusing my members. Talking to a member they think is still in the conversation.
This happens about never in my large community (partially because no one knows they have to). It only leads to members continuing to talk to members they think are still in the conversation.