There is indeed an issue with our code not honoring a bundle's icon. This issue manifests itself when using AppBundler and should be fixed.
SQL Developer, though, uses complicated procedure to launch itself: first, user clicks the .app, then a shell script gets launched, then an executable that, finally, launches "java" process. I've no idea how to distinguish this case for the case of user starting "java" executable via the command line. So, my recommendation is to add the following line to the sqldeveloper-Darwin.conf: