Kyoko and Chihiro as a duo? Yes!
[This can be seen as a romantic or platonic relationship.]
Honestly, these two are pretty different in character but they'd make a great duo. stoic, serious and mystery solving Kyoko paired up with the insecure, shy and computer smart Chihiro.
Kyoko: She tends to get paired with Makoto, Byakuya or Shuichi when it comes to detective work, but I have a new idea. Kyoko is the Ultimate Detective, she's highly intelligent especially in mysteries and puzzle solving. She's reserved and hides her emotions much opposite to Makoto, Chihiro and even Shuichi. Pairing her with Makoto is common, after all she was the mysterious support character in THH and did her part in the anime. Byakuya ends up tagging along with those two for being the antagonist and getting great character development, however you can see some where Makoto is not involved. Shuichi is an obvious pair, they both share the same talent and are a great duo alone when it comes to detective work. Kyoko is the moon to Makoto's sun and she's seen as Shuichi's teacher.
Chihiro: Chihiro, on the other hand doesn't get much shine when it comes to his own skills so he'll tend to be paired with people to help him get stronger like Mondo and Taka. However, this causes Chihiro's programming skills to go unnoticed, especially with how much help they could be with Kyoko's works but we'll talk about that later. Chihiro is the Ultimate Programmer, he's intelligent in technology and fast at coding. He's emotional and timid unlike anyone Kyoko is paired with. For this reason and his want to become stronger, he's constantly paired with Mondo to grow and Kiyotaka due to all of chapter 2. Sometimes, he's even paired with Chiaki for her love of gaming and Chihiro being able to make her one.
Now, how would they work? I commonly see them great as partners in crime- not in actual crime but more of solving crime. Kyoko, being an amazing detective can still use assistance and she can't always access certain information. Chihiro on the other hand, can access any computer information since he most likely knows how to hack into devices, confirmed with Alter Ego and a common headcanon among most. Kyoko can solve and gather her own information while Chihiro can gain extra information for her. Chihiro is also seen as timid among many, if he can gain enough confidence he could be a spy in a way for missions you see mostly in shows, undercover missions.
Outside of being partners in crime, they have much more to them. Chihiro can help Kyoko feel less insecure about her emotions and help her show them more; Kyoko can return the cover by helping boost Chihiro's confidence in his strengths. They do enjoy information and talk about things either related to or not related to their talents. They both enjoy listening and talking to others, I feel their conversations last hours and nothing can stop them. I think they'd enjoy quiet comforts as well, they're very quiet people themselves so the calm comfort of each other after a stressful day is something they might need.
They hadn't gotten much screen-time together, in fact they only did when they were with everyone else however I think there's some missed potential in the two. If there's any of your own headcanons or you wish to add something, please let me know!
[I might do more of these, would anyone be interested?]