More and more of us are using the
BigWigs Packager (thanks for all the help, Ketho!) which can create zips for all three versions of the game and upload to Wowinterface, Curseforge, GitHub, and Wago. I create one ToC file to rule them all, and for simple projects all you need is one .pkgmeta file along with your Lua/XML addon code.
If the addon gets a bit more complex, requiring addon code and/or .pkmeta files for each game version, you set it up once and forget about it. The initial bookkeeping for such complexity is a little tedious, but once you are done, it's done.