The earliest known Jew named Yom Tov lived in the Gaonic era (8th-9th centuries), and the most well known are the Tosafist Rabbi Yom Tov of Joigny (died in York massacre of 1190) and Yom Tov Lipman Heller (known as the Tosfot Yom Tov) who lived in Eastern Europe 1579-1674. 

The name means “good day” or “holiday”. I suspect the origin is in a translation of a similar-meaning French or German  name like Bonhomme/Guttmann (“good man”). 

Aside from being named for someone with that name, it may also connote a birthday coinciding with a holiday.