.bak isn't it's own filetype, it's just the conventional extension used for backups of other files. the pge editor backs your level up sometimes while you're editing it, and the uses could range from convenience to reverting certain operations or even as a failsafe in case of a crash, though you'd have to ask wohlstand if you wanted to know the exact details of what the level backups are for. from experience these are safe to delete.
JSON is short for javascript object notation, and they're essentially just a simple way to organize data in a plain text format. when you refer to a json file in your level folder, i assume you mean "progress.json". if i recall correctly, this file is used for achievement functionality within smbx2. read more on that
here. erasing it from an episode's folder will most likely just delete your achievement progress for that episode, though i haven't tested it myself.