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I think she was assuming that, as well as... The only explanation I can think of is that Shinichi's/Conan's memory is effectively distorting Shukichi. Even with shrunken Mary being the only character in DC (and that Shinichi/Conan has seen) whose hair is a match to the woman he sees, and even with Shinichi/Conan theorizing that Mary, indeed, was, like him, shrunk, he still hasn't made the connection—thus, I'd say Shinichi/Conan isn't that trustworthy when it comes to, at least, Mary and the middle brother... until he has his revelation moment, of course.