Don't quote me on this, but I believe that if V doesn't have a penis, Johnny has a line about it 'not being an issue for long' or something like that. Transitioning itself seems fairly standard in Cyberpunk setting - Claire was remarkable in that she chose to do it without cybernetics. All Johnny would have to do is see a ripper doc, and he'd have whatever he wanted.
Johnny's friendship does affect how he act towards V - he can forcibly take V's body, if their friendship is low enough and you choose certain endings.