As far as I understood what I googled up, metadata in archive are only stored when compressing a folder using Archiver utility. So, basically, when you create archive using "compress" from pop-up menu. They are created before, when you create a folder or a file. Metadata are stored in .DS_Store (Desktop Services Store) files.
So what to do about it? Solution is actually simple, use command-line zip utility to zip your folder and you should be good. Don't forget to delete metadata files .DS_Store before.
rm -rf `find . -name .DS_Store`
zip -r archiveName.zip *
test how unzip behaves
mkdir unzip-test
unzip archiveName.zip -d unzip-test/
if there are no .DS_Stores file and/or __MACOSX directory then you should have archive without metadata and you should be good to go without worries :).
Links
Wikipedia on metadata
Mac OS X Resource Fork and Command Line Tips
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