So maybe the concept is that following Space Seed, the records did reflect that Khan Noonien-Singh and his followers had been found, but the pertinent details as to what happened to them, which might allow anyone with an axe to grind to extrapolate where they had been dropped off (since again, that was an unprotected, unpatrolled area for no apparent reason, given all that canon has built up around the concept by this point) were kept secret to protect Khan and the Augments (again, rather than any kind of active observation of patrol that would also serve to keep tabs on them...) This would either assume that Starfleet has a very low opinion of its officers, or that they expect unclassified Starfleet logs to just be open to the general public. So there are still holes in the theory. But it, at least, makes a bit of sense with the reference to 'Chekov and an NDA' and all of that. Even if the automatic classification of logs for the dead part is still a head-scratcher, and the concept of Starfleet both classifying the logs because they are in some way concerned with the Augments, and ignoring Ceti Alpha V, seem mutually exclusive to one-another.