No need for new directories, you just rename the old recipe (or duplicate, rename, test and if it works, delete the old recipe).
Having the version in the recipe name has advantages. Obviously, you can see the version of the recipe without having to open it and look for the SOURCE_URI etc. Also, you may want to use the variable $portVersion in the recipe wherever you refer to the version (like in the SOURCE_URI, SOURCE_DIR etc.) to have it all auto-update when you change the recipe name.
"Nightlies" may be a special case, but I doubt you want to keep uptodate with a fast-moving app. But, for example, youtube-dl has almost weekly releases. Check its use of $portVersion to minimize the changes needed for each release.