> If my application depends on some of those zero'd fields, it seems like that has potential to cause serious debugging problems, as opposed to just causing an error on the parse.

if your app didn't used to handle the 'zero' case (assuming zero was a "valid" value for said field), then the app was poorly written and would'be been broken in the first place. However, if the app _did_ handle the 'zero' case, then the app continued to work! The end user would've been none-the-wiser about the change (mostly), and some time later, the app could be upgraded to ignore those known fields.

Causing a parse error would mean the app stopped working altogether. Much worse a result for the end user.