The latest release of tools.namespace depends upon java.classpath 0.2.3, which does not have the fix for CLASSPATH-8, which was first released with java.classpath 0.3.0 I believe.
Of course people can manually add a dependency upon the later version of java.classpath when they use tools.namespace, it would probably give a smoother experience if depending upon the latest tools.namespace by default depended upon a later java.classpath with that fix, e.g. https://ask.clojure.org/index.php/8288/java-11-and-tools-namespace
I have not carefully checked whether there are any issues with bumping up the java.classpath dependency version in tools.namespace, but have done a quick test with (refresh) in the test project at the link above and verified that it does improve the behavior there.
Bumped and released in tools.namespace 0.3.1.