It's possible the student records show that Miko is not actually a student at the school or if there is a "Miko", it's a completely different person.
I'm leaning towards the theory that there is no "Yashiro Miko" in the student register, mainly because I can't think what information her entry could contain that would allow Shiori to identify her as a fake. Things like address and date of birth aren't going to tell her anything, after all.
Also, here's something to consider. We've been assuming that Miko and Hinako are friends because they sit together in class, which is due to their surnames being next to each other in alphabetical order. But it's a pretty big coincidence that Hinako's classroom neighbour just happens to be the one who's been protecting her from anthropophagic monsters all this time, isn't it? What if Miko arranged that they would sit together in order that they would become friends?