You can remove JSON fields at the cost of breaking your clients at runtime that expect those fields. Of course the same can happen with any deserialization libraries, but protobufs at least make it more explicit - and you may also be more easily able to track down consumers using older versions.

For the missing case, whenever I use json, I always start with a sane default struct, then overwrite those with the externally provided values. If a field is missing, it will be handled reasonably.