Kudu was designed to be a columnar data store. Which means that if you had a schema like table PERSON(name STRING, age INT), you would store all the names together, and then all the ages together. This lets you do fancy tricks like run-length encoding on the age fields, and so forth.

There is also a Kudu RPC format which uses protocol buffers in places. But Kudu also sends some data over the wire that is not encoded as protocol buffers, to avoid the significant overhead of protocol buffer serialization / deserialization.

Apache Arrow is a separate project which started taking shape later. Essentially it was conceived as a way of allowing multiple applications to share columnar data that was in memory. I remember there being a big focus on sharing memory locally in a "zero-copy" fashion by using things like memory mapping. I never actually worked on the project, though. Developers of projects like Impala, Kudu, etc. thought this was a cool idea since it would speed up their projects. I don't know how far along the implementations are, though. Certainly Kudu did not have any integration with Arrow when I worked on it, although that may have changed.

Protocol buffers is simple and has a lot of language bindings, but its performance is poor on Java. The official PB Java libraries generate a lot of temporary objects, which is a big problem in projects like HDFS. It works better on C++, but it's still not super-efficient or anything. It's... better than ASN.1, I guess? It has optional fields, and XDR didn't...