Hm, I should address this...
First off... Shinichi wouldn't be mentioned. Minors in Japan are left out of the media when involved in a case like that. He would be called "teenager A" or something to that degree. And that is if it even made it to the papers. A high profile case like that would never make it because the police wouldn't let it. Not only that, but Yuusaku and Yukiko wouldn't want it hitting the papers, considering that the head of the Homicide division is a close personal friend of the Kudo family, the BO would have no means to check.
Secondly, bodies are moved by the police. And are not released until positive ID is made or sometimes until the case is solved. And if an unknown method of death was the cause, then they would have to hold the body until that could be determined. So not having a body in this instance is completely natural.
I think Pisco might know who Shinichi is, but not know anything else. Shinichi was all over the news papers, so not knowing him means you were blind to the news for a while. However the issue is more whether he knows the situation with Shinichi. We know a team of BO agents went to the Kudo's house to determine he was dead or not twice, and that Shiho went as the head of the project that was used to kill him. However, it would be safe to assume that she was the highest ranked member there. I see no reason why they would use high level BO agents to do simple intel. So the likelihood of him knowing based on that is slim, and Gin doesn't talk about whom he's killed. He probably reported to the boss, and the boss told the science division to investigate. Pisco probably wasn't involved in Shinichi's investigation in the slightest. So while Pisco can make the connection to Shiho, he cannot make any connection to Shinichi, since he has no reason to, nor any knowledge base that would allow him to.
tl;dr: The collective knowledge of the BO's operations is not shared. It seems to be on a need to know basis, and thus Pisco has no reason to make that jump in reasoning considering he probably didn't even know Shinichi was killed using APTX (which would be the only thing linking the two).