But, even with a hyper-awareness, anokata would realize that he could not evade assassination attempts forever, therefore he would only have it going on as long as absolutely necessary to allay any suspicions. And, as that kind of person would be extremely intelligent and perceptive behind the facade, he would be able to guage the reactions of the persons involved and call off the hit once his goal has been accomplished.
I am on episode 424 and I seem to remember at least one episode when Haibara failed to react to the presence of a Black Organization member. Additionally, anokata would be so deeply immersed into his cover and masking his presence, whether he is Kogoro or somebody else, that I would be surprised if she DID get a reaction to him.
I am sure he HAS realized Conan and Haibara's situation. The reason he doesn't send the Organization to kill one or both of them is simple. They are too close to him, so their deaths might draw undue attention, but they are close enough that he can watch them himself and know when they become a real threat making their elimination essential.
Your responses are incredibly weak because they fail to address why the boss would voluntarily putting himself in the line of fire, and how his actions make sense without omniscience. One of the things you don't know yet is that Vermouth has explained that the boss is "Cautious to a Fault". He is someone so careful that he is liable to break a bridge testing it to make sure it is safe to cross. Therefore an aggressive, fly-by-the-seat-of-his-pants plot that would frame himself and put his life at risk based on an unstable scenario where one of his agents suddenly disappeared and Conan is doing who-knows-what seems entirely contrary to his nature as Vermouth explains it. There are far too many unknowns. How would the boss know Conan would reach him in time and the distractions would work? How was the boss planning to call off Gin after Conan had tried and failed to distract them - when going to the window to yell at Conan exposes him more? It doesn't make sense.
Finally, do you really think hypothetical bossKogoro is unable to figure out how to make Conan and Ai have an accident that couldn't be traced back to him when he knows Conan's behavior intimately and has the resources of a whole Organization? Wave one whiff of a murder mystery in front of Conan and he runs off, and the Detective Boys are sure to follow, meaning the boss can easily put Conan and Ai into any sort of deadly setup he may like. Also, why wait to eliminate them when they are already making friends with ex-members and the FBI? Kogoroboss should have shut Conan down after interfering with Gin and Vodka on the train case, the one where Kogoro stayed on the train that the two MiB were trying to blow up, which doesn't make any sense. The plotholes don't pass scrutiny.
Also, in addition to what everyone else has said, before Vermouth dropped that line about the boss's personality, most people didn't think Kogoro would be the boss because it would be out of character. Gosho doesn't go in for "bullshit twists". Gosho is a plain vanilla by-the-rules mystery designer as evidenced in all his regular cases and arc cases to date. He has never once has done something dirty to lie to the reader, such as have someone who wasn't a suspect who hadn't made prior appearances be the killer. Even the misleading thoughts and dialogue always have a true context that makes sense and explains the choice of words.
Furthermore, Gosho plays fair because he wants his readers to solve the mystery, unlike the writers who employ bullshit twists because they want "no one saw this coming" or to defeat the reader. (Even though a major ally being the mastermind is such an overdone trope that it is charcoal. It's also why everyone and their mom starts by suspecting the protagonist's friends.) When you get there, somewhere in chapters 550-552 (hammer nail snake case) Conan roughly says that people often times really are what they seem, and that it's impossible to live a lie without letting the cracks of who you really are show through. Therefore, it would be out of character for Gosho to set up such a major premise "If the Black Organization finds out Conan/Ai's true identity, they and everyone around them will be killed", and then defy it by having a boss who did know but didn't act because of some handwavy, sketchy reason.