Questions, unlike statements, don't assert anything, so they can't be either true or false. Since the normal use for [negation][1] 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][2], 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.


  [1]: http://www.umich.edu/~jlawler/CELS-Negation.pdf
  [2]: http://www.umich.edu/~jlawler/tags.pdf