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I'm not really a Java dev, but I took some time to test the output of both java.util.zip.ZipOutputStream and org.apache.commons.compress.archivers.zip.ZipArchiveOutputStream. I used both to zip a file named 'õäöü.txt' and then tried to unzip it with the default application, i.e. whatever runs from context menu, on Windows 7 and Manjaro 0.8.10
Archive created with ZipOutputStream had a mangled file name when unzipped on both Windows and Linux. The same was true for ZipArchiveOutputStream when using only the default options. But by setting additional flags as described at http://info.michael-simons.eu/2010/01/05/create-zip-archives-containing-unicode-filenames-with-java/ the archive produced became readable on Linux. Even though it does not help me with my Windows problem, I consider this preferrable to current behavior.
Usage of ZipArchiveOutputStream would also allow to add a (maybe job specific) configuration option for setting zip archive encoding for those poor souls stuck on Windows.