The name became vacant after Clegane decided to paint the wall of the Red Keep with whatever he had with him.
Joke aside, Aegon would be named Aegon VI only if he would have been crowned.
Aegon, son of King Aerys II Targaryen and Queen Rhaella, didn't have any number, such as lot of other Aegons, like Aegon, son of Aenys I, who became the Uncrowned after his uncle usurped the Throne.
As Aegon, son of Rhaegar and Elia, supposedly died during the sack of Kings Landing, the last Aegon that ruled is still Aegon V.
Therefore, would Jon Snow claim the crown as a Targaryen, he would be the sixth Aegon to rule.