Haise Sasaki is Kaneki, and Kaneki's been gone for almost four years, yet Aogiri doesn't seem the least bit concerned about it, despite him being one of their captains. Do they think Kaneki's dead? I mean, Kaneki has disappeared without a trace and they do nothing to try and find him. What's more, if they thought the CCG had him, why not try to get him back? It's not like he's just an expendable henchman, he a freaking captain and he's a SS ranked ghoul! So even if they were just using him, that's plenty reason enough to go rescue him. Not to mention that he knows too much to just let the CCG have him. Am I just overthinking this, because it makes no sense.
During the Owl Suppression operation, the battle resulted in heavy losses on both sides. Many of the investigators were wounded or killed, and about 99% of the Ghouls were exterminated in the 20th ward. So both sides were still recovering from the loss and the missing investigators / ghouls were declared dead, missing in action, or captured.
According to wiki
While it was reported that no prisoners were taken, Ken Kaneki was taken into custody
Because of this contradiction in reporting, it seems that the higher up's in the CCG seem to have some plans for Kaneki (mainly Arima since he took responsibility for Kaneki).
Also, Aogiri members weren't given orders by any higher ranked member (they mainly are Eto, Tatara and Noro) to go search for Kaneki (or save him if they knew he was captured by the CCG).
Maybe the CCG plans using him to exterminate the Ghouls, maybe he is acting as a spy for Aogiri inside the CCG. Due to these possible theories, it seems like Kaneki is a part of some bigger plot. Thus you might not be overthinking, there could be a bigger game being played behind the scenes which you might have to wait for the anime to reveal.
If you are excited and cannot wait that long, then these spoilers are for you!
At an unspecified point, Arima found and defeated Eto Yoshimura at her shrine hide-out. Rather than simply kill the infamous One-Eyed Owl, he questioned her about her motivations and learned of her desire to change the world. Interested in her ideals, Arima spared her life and allegedly began to conspire in secret with her.
During one confrontation, Eto revealed her hatred for the world, criticizing its state, and saying the ghoul who killed Arima would be the hope for her entire race, while the latter smiled at her. They formed a plan to groom someone who would be competent enough to bear the title of the One-Eyed King.
so connecting the dots,
As the story moves on, both Arima and Eto finally find that someone. Someone who could change the state of the world, someone who understands both the Humans and the Ghouls, someone who has a place in both of the worlds - Kaneki is a perfect match for this role. Thus Eto and Arima help Kaneki to become stronger. Kaneki in the end becomes competent and trusted enough to hold the title of One-Eyed King.