Except they were sorta-maybe killed off because Kawamori doesn't want to revisit them.
They kind of DID have "the end" stamped on them, though. The TV series closed the story rather effectively. Most of Hikaru's plot in the TV series revolved around his romantic interests, misadventures, and screwups. Once you finalize all of that, there's not a lot left to do.
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yup, the series did give a sense of closure to the story going on between the three, and that would have been enough. but kawamori didn't want to stop there.
he says, "oh by the way, just to make things clear, they (hikaru and misa) eventually get married, misa gets command of a new sdf and hikaru goes along for the ride of course.well, minmei also kinda tags along."
and we say, "yeah, we kinda figured that out since it was implied with the ending of the tv series"
yup, all's well that ends well...there's still closure...
but then kawamori says, "oh by the way, some years later they go missing in the center of the galaxy..."
... What the F*#@??!
so, i agree that the main story has ended, but kawamori made it so that he left one final question mark as to the final fate of the three main characters and the whole crew of megaroad. either as a teaser, or, as you said, a final declaration that he will never touch on those characters again.