Note that just because you cannot manage a lot of jars through guix you can still maintain a java project that includes steps to build its source outside of guix.

Also for clojure heads the Nonguix[1] repository includes a leiningen package.

I think as time goes on and guix matures we will start to see more third party repositories that provide convenient builds of things. For instance I run guix system on a 2015 Chromebook Pixel and to do that I used the installation image provided at Nonguix to make sure I had all of the nonfree drivers I needed.

[1] https://gitlab.com/nonguix/nonguix