Currently, the :unused-namespaces linter reports false positives on code like
(require 'some.namespace)
(let [foo (resolve 'some.namespace/foo)]
...)
The above is quite common, especially if you have circular dependencies i think.
I don't think it would be too much work to find all namespaces used in clojure.core/resolve calls and include them in the set of used namespaces.