I've just come up with a wild theory.
Akemi might be Atsushi's daughter with Vermouth (?), and Shiho is Elena's daughter with Anokata (if the boss' male of course). I think that this theory explains a lot...
First, it explains why The Boss never ordered anyone to hunt down Haibara and kill her, despite the fact that she can spoil lots of information to the FBI/CIA/everyone (Please note that Bourbon's Sherry-hunting mission has not yet to be surely confirmed, as it's highly hinted that his target was Akai instead). In the Haido Hotel case (Vol 24), Gin noticed that Sherry has a "personal guardian". He didn't know about Conan back then, so he probably thought that Sherry has some kind of connection with the FBI/CIA/police/whatever... Gin's suspicion has been confirmed in the Ding Dong Dash case (Vol 48-49), that Sherry DOES have something to do with the FBI. Though it seemed like Kogoro was just a bait set up for them, the bug he found under Kir's shoe clearly "belongs to Sherry" (which means that Sherry has been helping the FBI). It is likely that Gin has reported this detail to Anokata...
Secondly, it explains Akemi and Shiho's different fates within the Org. If my theory is correct, then there might be a love-triangle (Anokata-Vermouth-Atsushi) LOL In other words, Anokata hates Atsushi, therefore hates his daughter (Akemi). Meanwhile, Anokata made sure that his own daughter (Shiho) is trained to be an excellent scientist, and has high ranking (unlike Akemi). Anokata probably got rid of Atsushi and spread the rumor that it was an accident (though I cannot explain why Elena died). Akemi, on the other hand, is much harder to kill, since she is his favorite woman's daughter, and if he had killed her with no reason, Sherry would have been pissed-off and gave up the project. Anokata could not come up with a suitable motive to get rid of her, until one event... Yes, Akai's betrayal.
And finally, if you've read all the above, you'll understand many of Vermouth's mysterious actions. Because of her daughter's death (current timeline) or mental pain (in the past), she held a serious grudge against Akai & Shiho (while she didn't even do anything to her). If I'm not mistaken, in the NY case, Vermouth was trying to lure out Akai (and kill him) on her own agenda, not the boss' order. Have you ever wondered why she was always waiting for a "silver bullet" to come, while Akai was still alive ? Comparing to Conan (who is only good in deductions), Akai also has skills and experiences, and he knows the Org. very well. It doesn't make sense when Vermouth waited for a "silver bullet", while still wanted to kill him at the same time (and it's before she met Shinichi). The reason behind it might be personal grudge... As for Shiho, the reason why Vermouth wanted to kill her so bad (that she flied all the ways from the US to Japan just to do this), was probably because she and her daughter were treated so unfairly (and maybe also because of her APTX-project). While Akemi earned nothing within the Org., Shiho had everything (educations, a whole lab, high-ranking...). While Akemi ended up dead trying to save her, Shiho's life is getting better and better (with Conan, Agasa, DB...).
And please notice that in Western countries, people usually call their child something like "my sweet angel", "my small angel"... Ran resembles Akemi + Vermouth named Ran "Angel", does that ring any bell ?
Problems about this theory:
- There is still no evidence about Anokata's gender, except for his/her interest in Vermouth, which may point out that the boss is male.
- It does not explain Elena's death.
- It does not explain Vermouth's unnatural youth and why she called the Miyano's project "foolish".
- If Bourbon's mission is really Sherry-hunting, then this theory doesn't stand well.