Mine has the hole. I had originally tied the stock filter housing into the cowl so when I started using a BHAF the hole was already there. I sometimes flip the insulation over the hole to quiten things down a bit and to tell the truth, I can't tell any difference.
I ran a stainless housing for a while on my BHAF (fully enclosed) that tied into the cowl and the factory fresh air duct, again, not a earthshattering amount of difference.
RJR