How do you go about searching the DB if everything is stored as a JSON object? Are you using an index like solr/sphinx instead of doing any searches directly in mysql?
We keep things we might need to search in regular columns (typically with indexes). The JSON object is just a way to add extra data to rows, which we can fetch and deal with on the app side. That works fine for a lot of things, and we're hoping it will give us some flexibility around when we need to do schema migrations in some cases.
Your DB should be cognizant of JSON. For instance, JSON records can be converted into key-value combinations that are then indexed.