Having an "explosion" that is only barely large enough to shatter the planet and then let it coalesce more or less back together would be a special case. Within broad parameters, yes, but still a special case of an even broader set. If we can postulate an explosion in the first place, we can postulate one that sends most of the rock in escape trajectories, or makes it cease to exist altogether. We have seen all sorts of such explosions already. The Species 8472 or Xindi weapons just made the planet go away; the two ways Praxis exploded in the two timelines both left half a world intact and the other half at least partially floating nearby. The DDM left behind dust and pebbles. While the death ray scenes never dealt with close celestial bodies one way or another (what happened to Luna in "Twilight", say?), none of these latter examples harmed other nearby (or indeed point-blank) worlds much... Timo Saloniemi
The Vanguard series offers another possible explanation, as does "To Reign in Hell". The former is more "this is what happened" while the latter involves speculation by characters. There isn't really a contradiction there in that the speculators aren't aware of the events depicted in the former (out-of-universe because the books hadn't been written yet, in-universe because the left hand didn't know what the right hand was doing).
The New Frontier books offer another version for the demise of CA VI. But while that one directly competes with and contradicts the Vanguard story, we could argue that it is a flat out lie, a cover story intended to keep the Vanguard truth from becoming public knowledge inside Starfleet. It is but a story in NF, after all, something told by a character but not actually "shown". Timo Saloniemi
Given the adventures he had under Captain James T. Kirk, Chekov likely had much better stories to tell than that one day they picked up some random 20th century criminal.
The thing is, we know from The Doomsday Machine that the sensors can very quickly scan a system and not only report the positions of the planets, but also spot "missing" planets and related debris. To assume that out of the dozens of parameters the sensors could almost instantly report (orbital distance, orbital inclination, revolution duration, rotation duration...) on a known planetary body, that the only one that anyone would pay attention to would be "desert-like" attributes is either wildly implausible or implies serious un-professionalism on the part of Reliant's crew.
Yet the thing actually established by the episode is that even if the sensors can do this, they don't. Remember how the crew came to realize that the planetary system was gone? By flying into the rubble. It was only after the paint job was ruined that Spock bothered to take a look at his instruments and tell his captain that the system's planets were no longer there. Subsequently, the ship had to enter "the limits of the system" to verify its presence or absence, system by system, until finally the ship reached the system where the Constellation was found. And still, Spock only scanned for the presence or absence of planets when "within the limits", and could declare the unexpected news that two of the planets still survived. So clearly 1) it is not standard procedure to scan in advance whether a planetary system is in place or not, and 2) even when this becomes a burning question, it isn't done until the ship is well within a system's "limits", and absolutely cannot be done from several star systems across. We can argue that Starfleet throughout its history has been harboring unprofessional nincompoops, and raising those to heroic status - or that starship instruments in fact can not achieve the things you propose they can. Given either explanation, it follows that "orbital parameters" would be of zero interest to anybody. It's too much pain to establish them, and they are of no damn use anyway, not for starships or their crews. Timo Saloniemi
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. 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 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.
"Captain, we've reached the coordinates of the Ceti Alpha system." "We're here to examine the desert planet. Which one is that? And where is it?" "Ceti Alpha Six, sir. That's odd. Its placement doesn't match the survey scan from 100 years ago." "But it is the desert planet?" "Yes sir." "Plot course. And make a note in the ship's log that once we're done, we update the survey scan."
^That kind of goes with the novelization IIRC, which basically said the data they had on the system was an old probe, and while it had a different count on the number of planets, that data was discarded precisely because it was considered to be from an old and consequently considered unreliable probe. No mention of the E's trip there, but it's hardly a stretch to assume Kirk had that "survey" classified.
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.'?
That doesn't seem like such a stretch if the only existing data you had on the system was old and possibly unreliable...
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.
... or you lived in a universe where stuff comes along and explodes or hurls around planets all the time ...
Any way anyone slices it, such obsessive claims of...boo-boo-isms meant nothing to the success of the main plot. Khan could have surfed from the planet on a rubber-band powered Frisbee, and no one would care about such an insignificant item. I mean, really, it is almost inarguable that if not for TWOK, no one would be talking about ST on this scale today, as it would have died with TMP. Imagine that.
What makes you think that Kirk did anything at all regarding the records of the system given his reasons for being there? I think it's very likely Kirk wasn't very upfront with Starfleet about what happened.