So, our mission, should we choose to accept it, is this : What is the most plausible explanation for this issue? It doesn't need to be scientifically accurate as such... just something that could at least make sense, kinda.And even if they didn't look up whether there were colonies on any of the planets for some reason, surely they would at least count the planets in the system when they arrived and notice one was missing!
Along those lines, the standard naming convention in Trek is (Star name) (order from the sun outwards). So Earth, being the third planet out from the star known as Sol, would be Sol 3. (They actually use Roman Numerals, but I'll use regular ones for the sake of simplicity.) Mars would be Sol 4, Neptune would be Sol 8, etc. Khan and his band were marooned on Ceti Alpha 5. Six months later, Ceti Alpha 6 exploded. Then the Reliant arrived, intending to investigate Ceti Alpha 6. Only since Ceti Alpha 6 wasn't there any more, they went to Ceti Alpha 5 thinking it was Ceti Alpha 6. So how does that make any sense at all? Even if the 6th planet is missing, how do you then mistake the 5th one for the 6th one? Wouldn't you still count out from the sun and then think that it's Ceti Alpha 7 that is actually Ceti Alpha 6? I mean, that would still be utterly stupid, because the 7th planet would still be in a completely different orbit than the place where the 6th planet was. But at least the problem then is that you didn't bother to look up the planetary orbits, rather than the fact that nobody on the ship can successfully count to six!
Of course, Khan does claim that the shock of the explosion shifted the orbit of Ceti Alpha 5. So are we supposed to believe that it shifted the orbit SO much that it actually moved Ceti Alpha 5 out right the way past the empty space where Ceti Alpha 6 was, then on out past Ceti Alpha 7 - which is the only way you could possibly think Ceti Alpha 5 was Ceti Alpha 6. But if so, then that's just absolutely ridiculous. Explosions in space don't actually produce a 'shock', because there's nothing for a shockwave to travel through. So you'd pretty much have to have a big chunk of Ceti Alpha 6 hit Ceti Alpha 5 with enough energy (and in the right direction) to boost its orbit right the way out to past Ceti Alpha 7. And do so without, say, smashing the planet into a million pieces when it hit it. And still leaving the environment of the planet survivable (consider the asteroid impact that wiped out the dinosaurs. Thosuands of times bigger that all the nuclear bombs built in the history of the world combined. This would be quadrillions of times bigger than that.) Which is impossible on just about every level.
And how does a planet just explode, anyway? Planets aren't made of dynamite! Earth has been around for a very long time, it's never just decided to explode!
As I see it, the explanation must cover these basic points.
Ceti Alpha VI must "explode". Prefereably, it must do so in such a way as to leave no traces of it behind (i.e., no asteroid belt.) Whilst they didn't say so, an extra asteroid belt left behind would have been kind of suspicious when the Reliant arrived.
Whatever happens to Ceti Alpha VI must shift the orbit of Ceti Alpha V. Other planets in the system may also have their orbits shifted, or not - Khan would presumably have no way to know what happened to them, so we can assume what we like.
The system must then be in such a state that a ship must be able to arrive and think that Ceti Alpha V is Ceti Alpha VI. I assume that even Paul Winfield takes enough time away from dying for the sake of white people to have learned to count at some point, so to me this says that Ceti Alpha V must end up as the actual sixth planet out in the system.
Whatever happens to Ceti Alpha V must damage the environment... but not so much as to make it uninhabitable per se. It was, from what we see, about like any Earth desert in the grip of a serious (quite possibly permanent) sand storm. As opposed to, say, being like the surface of Venus. To me, this means that we would ideally keep the orbital changes to it rather minimal.
I have a scenario in mind myself, but I want to see what others come up with before I post it!