I think there's a comparable difference in English between:
How do you not know? (你怎么不知道呢？) vs.
How could you not know [sth.]? (你怎么会不知道呢？)
It emphasizes the speaker's surprise, and comes off more as a rhetorical question: how is it possible that 你 doesn't know [sth.].
I asked Sage, and it came up with related 怎么会 examples:
怎么会下雨? (How could it be raining?)
怎么会这么热啊? (How could it be this hot?)
怎么会有人不喜欢吃巧克力呢? (How could there be people who don't like chocolate?)
他怎么会突然辞职？ (How could he suddenly resign?)
Like in the original example, it is possible to delete the 会 in all these examples to obtain grammatical sentences (although I think it'd be more common to add a particle in the first sentence, like 怎么下雨了？).