all, each, every, and both (and maybe some others with the same sort of inclusive meaning) are all less than optimal as subjects of a negated verb. The result is that English doesn't have anything that nicely solves the problem ____ aren't white . You're intuition about this is working!
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CalifJimThat said, people do say things like All of them aren't white. The astute listener will sense something not quite right. Does it mean None of them are white or does it mean Not all of them are white (= Some of them are not white)? There are cases where the ambiguity is not so pronounced, but even so
as long as we mean that all three are not Japanese, which is the meaning I'd take from this.
Anyway, I feel that sentences like "all of them are not Japanese" usually mean "none of them are Japanese" instead of "not all of them are Japanese", at least in speech.