I just noticed that jgoodies-looks doesn't install javadocs regardless of if you have doc in your useflags. I just looked at the ebuild and build.xml, and it looks like it should be installing.
Created attachment 61693 [details, diff] patch for jgoodies-looks-1.3.1-r1.ebuild I'm still not entirely sure why the original ebuild doesn't quite work. I patched build-1.3.1.xml to change where javadocs are put (build/doc/api), which means that they are installed in the right directory in compliance with the Java Policy. Also, I install a few more docs with USE=doc.
Created attachment 61694 [details, diff] patch for build-1.3.1.xml Patch for build-1.3.1.xml previously mentioned.
Fixed up the ebuild and build.xml; emerge sync and try again. Thanks for reporting this.