Junius was one of Rome's famous families. Lucius Junius Brutus is a legendary figure who goes back to the time of King Tarquinius, with another man of the same name more firmly rooted in history during the late Republic. Marcus Junius Brutus, of course, was one of Julius Caesar's assassins.

All men in the family were called Junius, all women Junia. Junias, as you mention, does not fit Latin naming conventions.

But of course the reference we have is not in Latin. It's in Koine Greek. I guess the question becomes one of transliteration. How did Greeks of the day write Latin names? (If the name is Latin, which it sounds like. I'm not really seeing the Johannes connection. Paul was Jewish and fluent in both Latin and Greek; I don't think he would have been likely to conflate an ordinary Hebrew name with a Latin-sounding one.)

Evidently, for many centuries Christians presumed the name was feminine, and it doesn't sound like they changed their minds for reasons of informed New Testament scholarship.