think about it this way, Obi-Wan's come in, he did a search probably a few times and it's not finding shit for him, so he asks her like "wtf this shit broke yo" and she's custodian of the greatest archive known to society, and she can't find it doing the same exact thing Obi-Wan probably did before asking her, then he has the gall to suggest somethings wrong with the library and she's going to scoff at him like he's nuts
i don't think Obi-Wan is well known outside the Jedi, he got quickly promoted because Qui Gonn was killed, he's got the apprentice nobody wants taught, he's not even a Master I don't think other than provisionally towards Anakin, he's like another step down still, so to the librarian he's like an instructor or maybe a visting professor coming in talking about missing planets in her perfect database
the library staff aren't designed to figure out why there's no planet there, just like they don't do your research for you in our modern libraries just find you stuff they have marked on the subject, that's why he's gotta go find an eight year old to solve it for him
the bigger question is what's on all those massive shelves, like nobody wants books anymore so they're all stored in a vault, but people expect huge shelves in a library so they just put up all these light things on them while you access everything through one of the few terminals shown
also i like how obi-wans datathing is basically a usb flash drive and he even yanks it out without going to "eject/safely remove hardware" first just force pulls it out from ten feet away