I can't recall any specific cases where Conan thought of a female suspect nude when there wasn't a reason not to (i.e. suspect found dead in bathtub). I'm not counting "shadowpeople" because that is how they are drawn regardless of whether anyone is thinking of them or not. Someone linked pictures of Conan and other people thinking of other characters nude as a counterpoint to the Gin example (can't find where though...), but most of them consisted of Ran when Conan thought she was actually nude, and there was a also a Sherry-haired shadowperson. Basically, Gin was thinking of Sherry naked for no particular reason at all (I doubt he would think she was naked at the time), and more explicitly than similar portrayals of people's thoughts. Gin was in fact surprised that Sherry planted the transmitter and made the first move. "Who would have thought that you would take action and approach me first?" This also shows that Gin is assuming Sherry is listening in on the other end... Haibara decided to go as soon as she heard APTX4869 was going to be there from Conan. Gin assumed that Shiho was the one listening in on the other end, and thus would have heard about the APTX 4869 directly. He didn't know she was following his and Vodka's dialogue secondhand via Conan. So Gin's read of her personality was right; she wanted to go to the party because APTX was going to be there. Gin didn't anticipate she might not have heard about the APTX at first so she initially refused.
There's probably a component of not wanting to be a danger to the kids, but preventing Ayumi from touching her at that moment isn't going to help. Also, it's uncharacteristic for Haibara to snap at the Detective Boys in relaxed conditions. Haibara was still in a reverie when Ayumi grabbed her arm. To explain it with another Detective Conan case (Coffee with murderous intent: chs 628-630, eps 513-514), Ran and Conan didn't want to eat Eri's gift cake after the case, despite both liking cake, because it reminded them of the tragic outcome. Basically, Haibara doesn't want to be touched at that moment because she was just thinking of something unpleasant related to Gin.