I know the code around this is pretty hacky (if use_zip_file then... instead of an abstraction). I know when it was added it was a bit controversial, I would be +1 on removing it. That being said I feel the entire DAG parsing process needs to be moved to the client-side (users who write DAGs), with a serialization scheme. I'm working on a proposal for this at the moment, and this would obviate even reading DAGs from the local filesystem.
Having everything zipped up gives us some assurance that when a DAG is > updated, the whole thing is replaced as a single unit. I don't believe unzipping files gives this atomicity guarantee any more than something like rsync --delete.
