It would be consistent that Starfleet lacks the ability to see whether a planet has exploded in a solar system, unless somebody goes there and takes a look. The plot of "Doomsday Machine" hinges on this, for example - as do episodes like "Way to Eden" where a starship foray is required to ascertain the presence and nature of a "mythical" world. Clearly, the Federation has some means of remote mapping, but just as clearly, these means don't allow for a resolution high enough to discern individual rock planets let alone their properties at any appreciable distance.
As for Chekov, it doesn't sound likely that he was even told about the outcome of "Space Seed". The whole Khan affair was really hush-hush, as we see Chekov later kept it secret from Terrell; we can assume it wasn't entered into Starfleet records, either, as otherwise Terrell would have found out about it when glancing over what the records told about his next target planet. It wouldn't be difficult to argue that Kirk and his top officers kept the details of Khan's marooning secret even from their own crew, in order to protect the innocent and the guilty alike.
...Kirk was a big Khan fan, after all, and we don't see much sign of the fan club dispersing even at the conclusion of the episode. The people present at the banishment court session (save perhaps for Spock) would all have an interest in protecting Khan against future discovery, for his sake as well as for their own. They wouldn't let the details leak to people not in the fan club, then.
Of course, it's equally possible that Chekov did know, but simply forgot. He's been to hundreds of planets and used thousands of others as navigation references, after all. It could and should all get a bit blurred in his head.
The third possibility is that Chekov did know but didn't worry much as he thought Khan was stranded on CA5, not on the "CA6" he thought his ship was visiting. If anything, Chekov could have been secretly cheering that Khan had blown up, or hoping that Khan would blow up when Genesis was detonated on CA6.
Timo Saloniemi