There's more to spatial navigation than picking a star and counting the number of planets on the way in. It seems pretty obvious that when a starship plots a course to a planet, the procedure would likely include determining where in its orbit the planet is going to be at a given time so they can intercet. For example, when Sulu plots a course to a destinaton, he uses a set of coordinates. If nobody has been there before, they could just set a course to the solar system in general and then plot from there.
However, since the Enterprise has
been to the Ceti Alpha system, it would have been catalogued and very specific information should be in the Starfleet database. They would have enough information to determine the coordinates of each planet and the numbers would be the same no matter what angle you approach them from (so they wouldn't be counting planets as they approached). Reliant should get to where Ceti Alpha 6 was supposed to be and see that it's no longer there. To use a Star Wars example, when Han Solo came out of hyperspace at Alderaan, there was nothing left but fragments. However, his coordinates took him to where the planet should have
been. That is pretty much how it should have worked for The Reliant.
The story implication is that the explosion moved Ceti Alpha 5 into the exact
orbit of Ceti Alpha 6. This is ridiculous. Adding to this, as stated upthread, there is no debris or any evidence that such a cataclysm has taken place. This is insane and almost inexcusable.
I say "almost" because there only possible explanation I can think of is that Chekov plotted the course himself, mistakenly and/or subconsciously chosing Ceti Alpha 5. Human error, particularly in Chekov, is always possible. A ship coming out of warp at the proper coordinates might not be paying attention to the rest of the system. However, since this weak explanation was not in the script, it's still a pretty sizable hole.