In classical Latin, the letters I/J and U/V were not differentiated yet. In addition, the distinction between upper and lower case wasn't there, either. The classical spelling is therefore
IVNIA. The modern spelling
Junia reflects what we know about ancient roman prononciation, note the the two classical Is represent two different sounds, the first a consonant (like modern English Y, not a soft G!), the second a vowel, and the classical V is in this case a vowel (like modern English OO). Since
Iunia is in many modern languages closer to the original prononciation, I think it is a legitimate spelling.