Questions, unlike statements, don't assert anything, so they can't be either true or false. Since the normal use for negation is to state that something is false, that means negation is not really needed in normal questions.
And that means that negation is available for other purposes in questions.
Language rarely wastes resources.
Negative Yes/No questions are used, like negative tag questions, to indicate the speaker's belief, or guess (the technical pragmatic term is invited inference), that the answer to the question is Yes. Affirmative Y/N questions have no such invited inference.
So, in this case, as Barrie has pointed out, the negative question indicates the speaker's belief that Jonny did in fact go bowling, and thus the question is asked as a matter of confirmation, rather than simple ignorance.