They both exist for a reason. JSON is really nice for your quick proof-of-concept where you have relatively few developers working on a small system. Up to a point, this also scales well.
On the other hand, if you have many developers, and the problem space starts converging toward scale, then certainly the problem space is different. Encoding of data cannot follow the language with the weakest type zoo, and efficiency starts to matter.
The hard part is to know when to make the switch, or when to anticipate growth in advance, such that you pick the right tool for the job.
It isn't just a question of the machine. For complex messaging, the added value of a well-defined message typing, provided by protobuf, will help. It will also remove a lot of problems if you have multiple different languages in the stack, talking to each other.