There are many people here who have had issues trying to decode the .zip files with a __MACOSX folder on even Mac OS 9. However, it is just AppleDouble encoding using a modified style of file naming, in a .ZIP archive. Which is decodable by using Decode AppleFile v1.1 on Mac SSW 7.0 and later running on a Macintosh Plus or newer.
Here is an example diagram using a Classic Mac OS extracted Mac OS X zipped file:
MacZip, which also works on Mac SSW 7 running on a Macintosh II (but not on a Macintosh SE or Macintosh Plus), was found out to be able to extract the modern .zip format of the archives that the OS X Archive Utility.app creates.
So now, folks who have old Macintosh computers to which they can download files from the Macintosh Garden, but experience issues transferring files from their modern PCs to their old Macs or don't have modern computers at all, will now be able to fix these "__MACOSX-messed-up archives", themselves.
By itself, MacZip does not understand the __MACOSX/._*-style of preserving Macintosh Resource fork specific information in a .zip archive using AppleDouble, it only understands it's own XtraStuf.mac/*-style of AppleDouble or raw ZIP content. You'll still have to manually decode the __MACOSX-style AppleDouble by using Decode AppleFile once the archive has been extracted by MacZip, to complete the reconstruction of these MacZip expanded files.
Further instructions for doing this are located on the Decode AppleFile v1.1 and MacZip pages.