There's a bunch of zip implementations(Info-Zip, Gzip, 7-Zip, PKZip, Pigz, etc.), so perhaps an older version of one of the implementations didn't support preserving the Linux executable permission in the past.
It never occurred to me before reading this comment that there actually is a use case for the execute permission. To me it was always just this annoying thing I have to do whenever I download an executable which I didn't have to do on Windows.