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1.Even so, the BO would have realised if their high ranking member turned younger won't they? This is the other reason Vermouth taking APTX4869 doesn't make sense; if they knew APTX4869 deaged people, the Org would have figured out how Shiho escaped. Atsushi and Elena Miyano may have started the APTX4869 project but the general project may have been started by someone else. Vermouth seems like she wants the Black Org to be brought down, but for some reason is unable to do so or does not want to do so herself. Rather than directly attacking the Org, she seems to have decided to give Shinichi and Shiho a fair and fighting chance to take he Org down and is helping them by keeping their secret and using her influence to keep them from being killed. (She saved Conan from being shot by Gin and co and Mouri Detective agency.) As for why she isn't completely loyal to the Org, it could be that over time her views and perspective have changed so she no longer sees eye to eye with the Org's mission. (Because of her anti-aging condition?) She could also be held “hostage” in some way. That conversation was by text message.

Back to the main topic, Gin and Shiho's relationship has been mentioned in the official Conan Drill guidebook (Specifically it's the relationship diagram on page 239). I moved the arrow legend to the top to save space. Note it was written before the conclusion of the Vermouth arc before Gin had suspicions about Vermouth being up to no good and keeping dangerous secrets. In case the image goes down, the text of the image is in the spoiler Gin's connection with Sherry which has led to his obsession over hunting her down and her hatred and extreme fear of him probably goes back to a relationship they had before Shiho betrayed the Org. Gin clearly knows Shiho personality very well as he can anticipate her movements despite having rather different lines of work. Shiho hardly knew most of the other agents in non-science related positions. She hadn't met Pisco since she was a baby, she had only heard of Korn and Chianti, and hadn't heard of Kir. Bourbon is new and thus doesn't count. Conan never asked about Tequila. Vermouth likely had a connection with the parents because of her apparent aging weirdness despite not being in science. Gin is on the business/assassination side of things, so it is anomalous how well he seems to know her given how she doesn't know much about anyone else outside of the research branch. They clearly have a connection outside of their professions to account for knowing each other so well. They must have spent lots of time together if Gin can identify her from a single hair with conviction. There are various possibilities for relationships between Shiho and Gin, like childhood friends (age difference could be an issue), mutual relationship or one sided attraction or abuse (Age difference again is an issue and that Shiho was in America until recently), mentor-mentee, etc. There is a strong case to be made for a romantic mutual relationship or onesided attraction using a good retranslation of the first chapter of the Reunion with the Black Org (the Pisco case) (file 24-7 or 238, ep 176) where the translator pointed out the innuendo Gin was using. (The retranslation was by kentaru). The retranslated monologue of Gin's in the dream is as follows: The translator also had a notes page from which I will quote a relevant section: Now, add this information to Gin's description of their meeting as a "reunion", him thinking of her in the nude, and Haibara yelling "Don't touch me!" when Ayumi places her hand on Haibara's arm, snapping her out remembering her dream. Furthermore, when the two of them meet on the rooftop of the Hyde City Hotel, there are more suggestive exchanges. Gin purposefully chose not to do his job in the most efficient fashion- shooting Shiho in the chimney- but instead chose to make a special exception for her by waiting out for her on the snowy rooftop because killing her there would be, paraphrasing, more beautiful. She even gets into the act by thanking him, albeit sarcastically, for "waiting for her in the cold"; Shiho seems to purposefully be alluding to the stereotypic scenario of one lover waiting for another in poor climate. Gin also makes a comment about her disguise, the uniform and the glasses, being unsuitable for her, which carries an implication that he thinks there is some other outfit which would be more suitable. In conclusion, I think there is significant evidence that they had a romantic relationship going on between them because I don't think Gin would, even though part of it is a dream, phrase things like that for the heck of it. The rooftop exchange seems to corroborate with Gin's dream personality. Whatever kind of relationship they had obviously didn't work out, probably because of Gin's messed up personality. Based on the fact Gin is still obsessing, Shiho was probably the one to dump him.