Thanks!
So the implication is that, when her husband died (though Gosho's statement on said matter leaves that up in the air), Mary had both Masumi's and Shukichi's surnames changed, and, around the time that he graduated from high school, Mary (and Shuichi, as well, perhaps) decided that Shukichi needed a new surname, for his own safety, while Mary would take Masumi to America (though that was much later on), and either found a married couple with surname Haneda, or just had the names made up (perhaps James played a role in this, in either finding willing participants to this ruse, or even altering records) so it would appear that Shukichi was not related to Mary, Shuichi and Masumi.
Though, if he's writing his real father's name down on a legal document that will be kept for records, then...
Alternatively, Serinox suggested, on DCTP, that Shukichi's envelope doesn't really contain a marriage registration form, since it was Shiho/Ai who suggested that idea, in the first place, and even referred to the idea as "cliché." The manager, if he knew Shukichi well enough (or even less, since Yumi probably doesn't know that much, if anything about Shukichi's family and background) he could fake it.
Instead, then, the old man may give us (and Shinichi/Conan) info about Shukichi's past by the end of the case—if this alternative theory is not so, and there really is a marriage registration form in Shukichi's envelope, then we may have Shinichi/Conan see the "Akai" part, without showing us that he saw that, and the last panel of the last page of File 947 will show us that, indeed, he saw that.