Emmanuele Bassi commented:
- Is it okay to use a single repo instead of gnome-nightly/gnome-apps-nightly split?
Yes; it definitely makes more sense to have the dependency for nightly apps come from the same repository.
- Is it okay to have a completely new name, say nightly.gnome.org/repo and mark older repos as EOL and ask people to migrate?
Yes, especially if the above holds true.