List of characters who know Subaru Okiya's identity
Conan Edogawa/Shinichi Kudo
Conan knew who Subaru was before they even first met, and also trusted him and lent him his house's keys despite Haibara's protest.
Yukiko is the one who taught Shuichi how to disguise himself as Subaru.
Yusaku seemed to be informed by his son about Subaru's identity. He even assumed the Subaru persona for one night to lead suspicious away from Akai.
James was the only member of the FBI aware of Akai's fake death plan as he noticed that Shuichi's fingers were coated by glue. It seemed he secretly kept contact with Shuichi disguised as Subaru.
Jodie was able to figure out the plan that Akai used to fake his death, and she managed to figure out Subaru's identity after been told by Camel that one of Akai's catchphrases is " The division of fault is 50/50", the same line Subaru used with Jodie during the Beika Department Store Case after he knocked her down preventing her from chasing after Scar Akai.
Camel witnessed Shuichi's disguise technique as Subaru Okiya as well as the Voice-Changing choker to modifiate his voice. After that he would give Akai a hand with guarding Haibara from the Kudo house.
During the scarlet showdown,Rei was able to discover the trick that Akai used to fake his death as well as Subaru's real identity and the voice-changing choker used to change a voice. But, Conan was able to deceive Rei creating a scenario where both Shuichi and Subaru, who was Yusaku in disguise, existed as different persons, which made Rei lose his suspicions. However, in Volume 90, Rei's suspicions had been aroused once again as he noticed Subaru is left-handed and remembered Yusaku disguised as Subaru is right-handed as he removed his cold mask with his right hand. At the end of the case , Rei seemed to have discovered Subaru's identity as he told the latter that he can't wait to pull out his high collar, but told him he won't do it until he obtains real proof. In chapter 1012, after receiving the order from Rum to investigate Shinichi, Amuro infiltrates the Kudo house where he is confronted by an unmasked Akai, confirming his previous suspicions.
There are four people who became suspicious about Subaru's identity.
Despite all of Bourbon's plans through out his arc, at the conclusion he seems to have convinced Vermouth that Shuichi Akai is truly dead. However, in Volume 90 she meets Okiya Subaru in person for the first time, while she is disguised as Azusa Enomoto. She seems curious and asks Rei who he is, which is when Rei notices that Subaru wrote left-handed. It is unclear how much Vermouth heard about Rei's comments to Subaru, but later she catches Rei staring at him. At the end of the case she gets distracted by Ran and it goes no further.
Ai Haibara/Shiho Miyano
At first, Haibara suspected Subaru to be a member of the Black Organization as she was able to sense the organization's smell from him. However, she changed her attitude towards Subaru after the latter reassured her during Detectives' Nocturne when Conan was kidnapped telling her "Don't make that kind of face, I will not let them run away", which caused her to remember something similiar to what Akai told her about her sister: " Don't make that kind of face , i will protect her at cost of my life". At that moment , Haibara begins to suspect that Subaru is Akai, she also have noticed that Subaru always wears high Collars despite sometimes the weather is hot. She even attempted to pull out his collar, suspecting that Subaru is hiding something under it (which is later revealed to be the Voice-Changing Choker).
Sera met Subaru during Yusaku Kudo's Cold Case and found him very suspicious. She have noticed somehow that Subaru is left handed as he was brushing his teeth with his left hand, which may have caused to remember her brother since Akai is left handed as well, however, her degree of suspicions is still unknown.
During the Antique Facet Case, they met for the second time, when Sera was trying to get her hands on the APTX 4869 antidote by investigating Haibara. During the case, Sera was trying to pressure Haibara into revealing her true identity and giving her the drug that restores " the flow of time". However, Subaru ended up interrupting Sera's investigation, which irritated Sera and tried to kick him. Subaru easily dodged the kick and told Sera that the divison of fault is "50:50"; saying that he might be at fault for irritating her, but she is also at fault for trying to kick him, which surprised Sera. At the end of the case, Sera asks her mother Mary about her "50:50" catchphrase, Mary said that it is a line that her husband used to say and her son Shuichi inherited from him. After learning the truth about the catchphrase, Sera started to suspect that Subaru is her brother Akai.
Hidemi helped Akai faking his death. However it is unknown if she is aware of his new identity as Subaru Okiya, but she does have his phone number, which she used to inform him of Rum.