We hit this in af and zu in gaia-l10n. Dwayne is going to try to fix his scripts, so he doesn't barf on empty repos, but we may still hit this. Given that this is the first time we've seen this ever, this might not be a pressing issue. However, given our change in how we pick up new repos to sync, this may be an error case we need to catch gracefully. It might be nice to get a periodic error/warning email about this, but nothing urgently actionable.
fwiw, legacy (handling l10n currently) considers empty repositories completely legitimate. In fact, it will translate non-existent upstream repos into existing empty repos. I think legacy behavior is what we want in general, as it allows pieces of the syncing system to be set up in parallel with the upstream repository creation and population.
We don't have to deal with this anymore, as vcs-sync only handles gecko-dev now.