Hi Timur,
The problem with JavaDoc is that it's a source-level attribute, so in order to be used from a Java editor the editor would have to understand Clojure. This is actually possible in Cursive - as far as I'm aware no other system does this right now. The other aspect would be generating JavaDoc HTML when offline documentation is produced - I don't know if the javadoc tool is extensible in order to allow this.
However the bigger issue is that most of the elements exposed to Java don't support any documentation. definterface, gen-class, deftype & defrecord do not. defprotocol does, but the interface generated from the protocol is really an implementation detail, I don't think it's intended to be used for interop. Some new commenting convention would need to be developed.
For all these reasons, I generally recommend defining your interop interfaces in Java and just implementing them in Clojure.
Cheers,