I don’t have an answer for Clojure.
Generally, Guix is able to install libraries into a system directory and point the language’s compiler/interpreter at that location.
If you are a Guix person and you use Python, we put the Python libs that you install through Guix into a directory that’s part of site-packages. As a Python developer I can either choose to use those libraries or I can use tools from my language community (e.g Pip and env) to ignore the libraries that came with the ‘system’.
Why shouldn’t it be possible to do the same thing with Clojure?
I agree that if you’re shipping tools they need to be up to date. That was what I thought was going to take a couple of hours when I started looking at this last week 