Well, first of all, quite a number of creatures are omitted from the version of Fantastic Beasts published by J.K. Rowling. No thunderbird, no swooping evil, and so forth. I suppose one could argue that they were redacted, but Rowling has mentioned (on Pottermore) various other creatures that would seem to meet the criteria for “beasts” as laid out in Fantastic Beasts and Where to Find Them, yet are not mentioned.
Perhaps the textbook that we have is not the Fantastic Beasts that people really use in HP. Perhaps, for example, it was redacted for publication for the non-magical community.
But more relevant to this particular case, the evidence suggests that Newt does not consider the Obscurus a "creature" or “beast”:
MADAM YA ZHOU: You know which of your creatures was responsible, Mr.
NEWT: No creature did this . . . Don’t pretend! You must know what
that was; look at the marks . . .
ANGLE ON SENATOR SHAW’S FACE.
ANGLE ON NEWT.
NEWT: That was an Obscurus.
Fantastic Beasts and Where to Find Them
Since the Obscurus is a manifestation of the subconscious of a witch or wizard, and can indeed be spoken with and reasoned with to some extent (as we see at the end of the movie), it seems possible that Newt considers it more being than beast.