I dont know much about cav in general and even less about horse archery in particular so I might be wrong here but isnt HA the nr1 anti lancer class? And if lancers have a hard time taking down a HA why would a HA ignore that target. Little risk of getting killed yourself and no spasmic unpredictable movments like you would get from inf. You would also support your team the best way you can (most of the time) by removing the enemy cav.
My tiny experiance of horse archery is that with enemy cav still around you will get lanced or slashed to death from behind if you're focusing on inf so its always best to try to dehorse or kill the enemy cav first. Both for your own and for your teams sake. Buffing HAs might indeed counter cav just as giving the lancers the lance angle back might also be a counter to cav.
BUT I agree that HA is fine (or was when I last played) though for another less anti-cav lobbyismic reason which is too far off-topic so I wont go into it in this thread.
On Topic: Arrows going through enemies chests/throats, different aimingspots for different maps, different aimingspots depending on your opponents ping, lag issues and funky hitboxes is what every archer mounted and on foot experience at times. I think there was a thread about it way way back in the technical problems section. I started to notice alot of these things when arrowspeed and later damage to head/body was tamperd with and it was like that untill I stopped playing (Då träffade du så dåligt Saffran att du inte märkte av detta
) Just like Buba I have no proof of this, its just a feeling.
When it feels like the aim is off I shoot a few refrence arrows at Chagan or Kerrigan (any GK lancer on your team will do) so I know how to adjust.