Hidan still hits the same way for me. I just completed my run of difficult mode an hour ago, so I can confirm this. Luckily I actually recorded my run and posted it to show what a run with over 3700 score might look like. You can check it out here: https://www.youtube.com/watch?v=Djfp60eG9e0

In the end, who hidan hits depends on where you place your ninjas and have your clones generated. He always hits the topmost row first.