I'm wondering why people are even thinking that April or his ship is even going to be in the new movie at all. Those comics are just tie-in merchandise that has little or nothing to do with the movie's plot. Just like those tie-in comics from four years ago had little to do with the plot of Star Trek '09. Did we see the TNG crew in that movie, even though they were in the comics? No.
I dunno, the Countdown comics were pretty essential if you wanted to see Nero as anything more than a crazy man obsessed with killing Spock for no apparent reason.
That said, Countdown into Darkness doesn't seem to be necessary for understanding what's going on or why things are happening, but it does seem to be setting up character threads for the film (particularly Spock).