Those flags should work fine on OS X.
I have a command aliased that gets rid of all the .DS_Store files that I run first. I then run the first zip line exactly as Jellby has it listed. For the second pass at the zip I use 'zip -r file.epub * -x mimetype'. Default compression settings are okay with me, and I'm assuming everything else in the directory should end up in the ePub anyways (I clean the directory up beforehand). The extra file attributes don't seem to cause any problems (unlike with the mimetype), but I should probably go ahead and add the -X into the second zip command anyways.