Unfortunately WoWI does not have any way to pull in libraries when packaging from a Git repo, so it's only usable if (a) your addon does not use any libraries or (b) you hard-embed all the libraries your addon uses. Note that (b) is bad, and you should not do it, since you will quickly end up shipping outdated libraries or wasting tons of your time keeping track of library updates by hand.
I'm currently letting the Curse packager make my ZIPs, since it can pull in libraries from any type of repository, and manually uploading them to WoWI.
Previously I was using SVN and letting WoWI's packager make my ZIPs, since it can pull things in by using svn:externals and nearly all libraries are in SVN repos, and manually uploading them to Curse.
Manually uploading to WoWI is actually much less painful than manually uploading to Curse, so even if I went back to SVN at this point (very unlikely) I would probably continue packaging on Curse and manually uploading on WoWI.
There is also the
WoWI Mod Uploader script, but it is rather outdated by now, and when I tried to use it a few months ago to automate uploading my Curse ZIPs to WoWI, I ran into issues on both ends since both sites have changed since 2010 but the script has not. It may work for very basic stuff, though.