My intuition is that there's a lot of important work to be done using logical representations of models and transforming them back and forth using well understood semantics operators. Deep functions will be part of said models, but the whole model does not necessarily need to be deep. We can already see hints of the field going in this direction in deep generative models [3].
[1] http://web.stanford.edu/class/psych209/Readings/LakeEtAlBBS....