The more I think about it, the less I realise I know about the role, but I'll note what's in my head at the moment.
What does a HoYD's attributes actually do? Do they ensure that he brings through better players?
The JPA and JPP attributes are, primarily, scouting attributes. In the case of the HoYD, are they used for bringing in better players? For example, will someone with JPA - 7 and JPP - 7 bring in better players than someone with JPA - 18 and JPP - 18?
What do we know?
We know that a higher youth recruitment rating allows you to cast your net wider, in turn, potentially helping you pick up better players.
We know that better junior coaching increases the CA of the players that enter your youth intake.
We know that the better your youth facilities, the better the 'training centre' for your players to develop.
As far as I can see, the HoYD's attributes (JPA and JPP) are purely used for assessing the players that enter your youth intake. Obviously, the higher the attributes, the better the judgement.
Once they enter your youth team (20's etc.), the report on their potential is given by your assistant, which is why I, and others, will have seen differences between the intake rating and the rating once they are signed.
Your HoYD will also affect the players coming through by their preferred formation and personality but, as far as I can figure out, without any concrete evidence, not their potential.