Is this omission enough to doubt the historicity of the story, or is there more evidence? Couldn't there by various reasons for the omission, thus not serving as proof for it being fictitious?
Josephus didn't necessarily record every deed Herod did. But Josephus hated Herod and catalogued a horror show's worth of crimes. Killing some kids because of a prophecy is exactly the kind of thing Josephus would have loved to lay at Herod's feet. One Josephus' themes on Herod was how paranoid he was about claimants to the throne. He catalogues a series of murders to finish off the old Hasmonean dynasty and against his own family. If Josephus knew the story of the Slaughter of the Innocents he likely would have included it. So it may be significant that he didn't.
The next piece against the slaughter is that it is possible that Bethlehem may not have actually been occupied during Herod's time. Aviram Oshri and other archeologists have found no evidence that anyone lived there at the time. It was occupied a century or two before, and it was occupied a century or two later. But it may not have been occupied at the time. Hard to have a slaughter, if there's no one there.
Finally the slaughter story seems to be an invention of Matthew. It isn't mentioned in either of the other Synoptic gospels. And Luke actually has an entirely different and incompatible story. The problem the gospel writers had was that their messiah was known to be from Galilee, and they had a firm prophecy that he had to be born in Bethlehem. So we got two different stories about how he was born in Bethlehem and how he moved to Galilee. The fact that Matthew includes an otherwise unknown horror by a known perpetrator of such horrors, isn't very good corroboration. The fact that it pits his legitimate heir to the throne against the evil hated tyrant occupying it doesn't help. Instead it makes it sound more like a "just so story." It's like including Queen Victoria in a story set in 1880 London. She may not be amused, but the audience will be.
That's where we end up, we have no evidence that it ever happened, circumstantial evidence that it didn't. And our source has a strong motivation to make up just such a story, leaving us with good reason to suspect it never happened.