The problem went away with all optional fields so it was decided the headache wasn't worth it.
I suspect that not having nullable fields, though, is just a case of letting an implementation detail, keeping the message representation compatible with C structs in the core implementation, bleed into the high-level interface. That design decision is just dripping with "C++ programmers getting twitchy about performance concerns" vibes.
Then proto3 went and implemented a hybrid that was the worst of both worlds. They made all fields optional, but eliminated the introspection that let a receiver know if a field had been populated by the sender. Instead they silently populated missing fields with a hardcoded default that could be a perfectly meaningful value for that field. This effectively made all fields required for the sender, but without the framework support to catch when fields were accidentally not populated. And it made it necessary to add custom signaling between the sender and receiver to indicate message versions or other mechanisms so the receiver could determine which fields the sender was expected to have actually populated.
This is very solid with message types, but for basic types you can add `optional field` if needed as well (essentially making the value nullable)
Proto3 made primitives all non-optional, default 0. But messages were all still optional, so you could always wrap primitives that really needed to be optional. Then they added optionals for primitives too recently, implemented internally as wrapper messages, which imo was long overdue.
Protobufs generally respect this property, but required fields break it. If you have a field that is marked 'required' and then a message omitting it passes through a server with that schema, the whole message will fail to parse. Even if the schema definition on both the sender and the recipient omits the field entirely.
Consider what happens when you add a new required field to a protobuf message, which might be embedded deep in a hierarchy, and then send it through a network of heterogenous binaries. You make the change in your source repository and expect that everything in your distributed system will instantly reflect that reality. However, binaries get pushed at different times. The sender may not have picked up the new schema, and so doesn't know to populate it. The recipient may not have picked up the new schema, and so doesn't expect to read it. Some message-bus middleware did pick up the new schema, and so the containing message which embeds your new field fails to parse, and the middleware binary crashes with an assertion failure, bringing down a lot of unrelated services too.
You could (e.g.) annotate all key fields as IDENTIFIERs. Client code can assume those will always be set in server responses, but are optional when making an RPC request to create that resource.
(This may just work in theory, though – I’m not sure which code generators have good support for field_behavior.)
I think the main problem with it, is that you cannot distinguish if the field has the default value or just wasn't set (which is just error prone).
However, there are solutions to this, that add very little overhead to the code and to message size (see e.g. [1]).
I don't get what part of your link I'm supposed to be looking at as a solution to that issue? I wasn't aware of a good solution except to have careful application logic looking for sentinel values? (which is garbage)
Re: your question, for proto3 an field that's declared as "optional" will allow distinguishing between set to default vs. not set, while non-"optional" fields don't.