Interestingly, Akako Koizumi calls Shinichi Kudo (without knowing him personally, though) a "magician" in the Black Star story, just like Masumi Sera later does in his own series.
The unnamed clock tower Kaito Kuroba and Aoko Nakamori had their first meeting in front of and which is the focus of Kaitou Kid's heist during Black Star is based on the clock tower of the Koriyama Public Hall in Koriyama City, located in the Fukushima Prefecture, with the main differences being that the upper part was changed to the place where the bell is integrated and a bigger clock face. The clock was removed for a long time until it was reintegrated into the tower in 1998, possibly inspiring Gosho Aoyama to his story in 1999.
Chapter 23-24 are a direct crossover with Detective Conan. Akako Koizumi foresees a person "from the east" who could be able to stop Kaitou Kid, who is later revealed to be high school detective Shinichi Kudo, accompanying inspector Juzo Megure in a helicopter of the Tokyo Metropolitan Police Department. Despite causing several hardships for Kid, he doesn't manage to catch him in the end, not even learning his name, in a foreshadowing of their first meeting in person as Conan Edogawa on the roof of the Haido City Hotel in his own series.
The story of chapter 27-28 happens on a Friday the 13th, just like FILE.605-609 (Volume 58, File 8-11 and Volume 59, File 1) of Detective Conan, which were released less than half a year apart, perhaps subtly hinting for them to be happening concurrently.
In the Omake after the "filming" of the 28th chapter of Magic Kaito has wrapped, the meta-fictional "child actor" of Kenta Connery is said of having to go to another shoot right now, which is revealed to be Detective Conan, with Kenta's actor also playing the role of Conan Edogawa.
The bird Kaitou Kid, disguised as Paul, conjures out of is top hat during the Hopper Magic Show in chapter 22, is Shonosuke, Yaiba Kurogane's pet vulture.