I think you have all currently existing stone plates.
From the update post about Naomi's CG scene: "At the secret prison, when you go to the cell area directly in front of the spot between the two guards, a new event will trigger if you had the Shanna/Naomi onsen scene and had the events with Cookie and the magic spirit."
After raping her at the police headquarters, you can later find her again at the bar of the thieves guild. Once you finish her events there, she'll disappear. That's the current end of her bad path events.