They don't count. Bookies would never pay out a golden boot bet while counting pen shootout goals. They're far too greedy.
They don't count for official records either. Penalty shoot-outs aren't technically part of the match result, they're just a way of picking a winner, as a coin toss was before pens were introduced.
Lukaku needs 2 goals in two games and Griezemann or Mbappe would need 3 in two just to draw level on 6. Kane has possibly already got enough, plus as I'm pretty sure the 3rd place play-off counts for the goals too then getting to the semi final secures 7 games whether yo win or lose so from a golden boot point of view we really don't need to get to the final!