It's not ideal, but it's not a cryptographic risk.
Using an encoding that (like Protobuf) has multiple representations for a message may cause you problems if you switch implementations - sha256(encode(msg)) might yield different hashes on different implementations of encode().
But the main risk is an encoding that has multiple interpretations of a single encoding (e.g. sha256(encode("admin", "true")) == sha256(encode("admint", "rue"))), and Protobuf (can be unserialized, and thus) doesn't have that problem.
Comments
It's not ideal, but it's not a cryptographic risk.
Using an encoding that (like Protobuf) has multiple representations for a message may cause you problems if you switch implementations - sha256(encode(msg)) might yield different hashes on different implementations of encode().
But the main risk is an encoding that has multiple interpretations of a single encoding (e.g. sha256(encode("admin", "true")) == sha256(encode("admint", "rue"))), and Protobuf (can be unserialized, and thus) doesn't have that problem.