I implore you to NOT use JSON or ProtocolBuffers, neither are appropriate formats for configuring my shell, or storing long sets of textual data. Protocol Buffers is hardly the kind of format I want to parse and read my history in, and JSON is a less than ideal configuration format for many reasons.
https://github.com/vstakhov/libucl UCL (Universal Configuration Language) is a much more appropriate format for configuring programs than JSON, and is has been accepted as standard for use configuring all tools included in the FreeBSD operating system.
I also suggest you consider using a different language to store shell history, since shell history and shell configuration are two very different jobs with different goals and trade offs. I personally would suggest a simple safe format like TOML https://github.com/toml-lang/toml for storing the history.
But If you do want a single format for both configuration and history, I would implore you to pick TOML not JSON or Protocol Buffers.