Indeed, I personally don't understand "你也不会呢？" as a native Chinese speaker. I'm not quite sure what you want to express here. To me personally, it's not just a matter of it being natural or not since I didn't understand this sentence. Also disclaimer, as a Cantonese user, my opinion could probably deviate from Standard Chinese users.
What comes to my mind initially of what you might want to say is "Don't you also don't know how to do it?"/"Aren't you also oblivious to how to do it?" which I would use "你不是也不會嗎？"?
But after reading it several times, it seems your Mom wanted to use a rhetoric 1. "Don't you also not believe in me?" or 2. "Even you also don't believe in me now, is it?" which I would use 1. "你不是也不相信我嗎？" or 2. "現在連你也不相信我了，不是嗎？"
So analytically, 會 here should carry the meaning of "could", as in "could believe" (會相信), but the clause before did not have the phrase "會相信", so I'm guessing this might create a dissonance in understanding what was implied after 會.
Then I also failed to find a case where "呢" could be used in situations like these, but I believe you wanted to use it in a rhetorical case. However, "嗎" should have been used. Not sure why though. It just sounds weird to me. Might still think about it and come back. (But still, I believe "unnatural" sentences are actually violating some grammatical rules, since descriptive grammar describes the pattern of how people speak.)