As stated many times he hid it in rukia BEFORE he left SS over 100 years ago when she was a kid living in the second worst area of SS. Azein found out it was hidden in her but she had disapeered on earth thanks to the power draining body that Urahara gave her, so he had the order for her arest and exicution placed.
As for if Ishin could see Rukia or not in the first chapter, I pesonaly belive that he could, he showed up in Ichigo's room seconds after she did and Urahara showed up rather quickly as well. The only things we know for sure is that he has not been able to go in to shinigami mode for about 20 years. he a captain's level of control over his powers. Rukia didn't seem to have any problems seeing spirits when she was near powerless in a veriation of the same type of body that Ishin was in. But reguardless even if he could not see her he had to have known about her by the grave vist and had reagianed his powers by the SS arc..
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In MIR if you do remember his last diaglogues pretty much indicate he has some idea but Isshin isnt 100 % sure . If he did sense hollow/shinigamis then he would have come to the rescue of Karin and Yuzu during MIR/GF Arc .
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It sounded to me like he was completely sure that Ichigo was Kon by that point and if he was only able to sense/see hollows and shinigami at that point but not use his powers what is he going to do? get in the way of the 2 (3 in the anime) people that can do something? We all saw what happens when someone does that. He's not Ichigo.
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Higurashi: Its a bit like watching a trainwreck, except you keep getting to see different trains wrecking with roughly the same passengers, into a variety of different objects. Also, the trains are driven by monkeys. On LSD.