It is not an anti pattern, it is the way most low level libraries and clojure itself are written.
Clojure is a tool, not a cult. This core team worship is turning people away. The core team made plenty of mistakes, and got called out, rightfully.
Most libraries are absolutely not written in this way either. Please point me to a single library that's actually written in the style you describe. The use of protocols in actual popular libraries like Ring tends to be minimal.
The reality is that dynamic typing has never been a real problem in Clojure. I've worked with the language almost exclusively for over a decade now, and I maintain a number of popular libraries, like Selmer, with millions of users.
Clojure gives you the option to run the compiler at runtime, so that's what people normally do. However, you can also run the compiler at compile time. Right?
For people who want type checking, they can opt to write Clojure in this defprotocol everywhere style, and turn on AOT. Then they basically get the same thing as what Java gives them.
As to example of libraries that are defprotocols everywhere, you should look at any of the low level performance minded libraries in the Clojure ecosystem, they are either written in this defprotocols everywhere style, such as nippy, neanderthal, dtype-next, and so on, or mostly in Java, such as http-kit, fast-edn, etc. I noticed this phenomenon, because my own libraries, editscript and datalevin, are written in this way. I take comfort that my fellow performance minded library authors are doing the same. Finally, isn't Clojurescript entirely driven by protocols?
So really, there are two kind of Clojure programmers. One type writes application code or high level libraries, and they write normal Clojure code all the time. However, there are also those who write primarily low level library code, which are used by the first camp, and their code is full of defprotocol and deftypes. So defprotocol everywhere is not anti-pattern. It's anti-pattern only in the mind of the first camp of programmers, and that's a narrow minded way of looking at things. Even the first version of Clojure Programming book by the core team members, are written in a way that's full of defrecord. Remember?
This "everything is a map" orthodoxy is turning people away from Clojure. Just let people write the code that suits their own needs. We can use more people who are pragmatic instead of dogmatic in the Clojure world. If you trust Rich Hickey's judgment, then you should trust him put in the features Clojure has for good reasons. Macros and protocols are part of the Clojure language, and you should be using them when the use case calls for them. Stop the "anti-pattern" nonsense.
These libraries aren't using protocols for type safety though, they're using them as a performance optimization. That's certainly a perfectly fine reason to use protocols, and I agree that it's a completely legitimate use case. It's the whole right tool for the job thing. If you're writing something where performance is the top concern, then that's what protocols are for.
I very much agree with you that that there are people who focus on low level code, and those who focus on application level code. The style of coding will be different depending on the type of problem you're solving. You're right that I failed to qualify my original statement regarding protocols being an anti-pattern.
You're absolutely correct that we should take a pragmatic approach towards using language features. Hence why the context of whether protocols are the right tool to each for lies in the type of code you're writing. And of course, some people find it easier to have more structure to help with their reasoning. Although, I'd argue tools like Malli work better there.
To sum up, I'm not arguing against protocols being useful or that there's no place for them. We started this discussion talking about whether protocols provide equivalent guarantees to Java's type system. I disagree regarding that. However, I also don't think that this is a real problem. Otherwise, use of something like core.typed would've become prevalent by now.
