But... that's not the way it happened. Kirk took Lt. Palmer's report on the distress call, then Sulu began to say he couldn't locate something while fiddling with the center nav plotter thing, then Spock spoke up from his sensor hood to say the system had been destroyed, then the debris appeared on the main viewscreen.
Yes, and this happened when Sulu said they were "within the limits" of the system. Neither the debris nor the absence of planets that was the cause of the debris were detected
until Spock deigned to start scanning for these things specifically - apparently because of Palmer and Sulu's failure to accomplish the mission the easy way, by tracking the SOS.
I don't know what "the limits" have to do with it, since Reliant is still mis-identifying Ceti Alpha V when "on orbital approach."
"The Doomsday Machine" shows that no scanning takes place before a starship enters these "limits" (thus debunking your original claim that such things are bread and butter for starship ops) - but not that scanning would take place at any later stage, either, not without a special reason. And it's very difficult to find other TOS references to idle scanning of a star system, too.
The point is, the technology appears to be plenty sufficient. But if you find it plausible that a starship on a survey mission with that equipment readily at hand would not employ it, would not notice the absence of a destroyed planet, and would navigate to the wrong planet, I'm not here to change your mind.
But the easy out there, and the one you for some reason refuse to consider, is that scanning is a major bother that is
not trivially achieved.
Sure, technology can achieve stuff. Doesn't mean it would be employed without good reason - and this is generally because it carries a price tag. Refusal to scan is no different from the equally odd refusal to employ shields except when no other alternative remains. And since we know nothing about how these "sensors" and "shields" actually are supposed to work, we really have no leg to stand on if claiming that they are used "incorrectly" or "insufficiently".
Isn't that a bit like them showing up in our system and going 'Heh, Neptune is looking a different size and is in a totally different position. But it's a gas planet, so it must be right.'?
The major difference is that people care about Sol. What's there to care about Ceti Alpha?
It doesn't wash that the NCC-1701 would either generate an unreliable survey of the Ceti Alpha system or allow one to stand in Starfleet records.
Why would NCC-1701 create a survey? That's something Kirk would have to enter in his logs, and he doesn't want to make any logs of the event. Not when he chooses to conclude those events with the act of hiding Khan from the authorities.
More significantly, we never hear of the hero starship creating surveys unless that is the specific mission of the ship. Professionals don't dabble in hobby projects when they have jobs to do.
UHURA: Record tapes engaged and ready, Captain.
KIRK: This hearing is now in session. Under the authority vested in me by Starfleet Command, <yadda yadda>
...And that's what data shredders are for.
Timo Saloniemi