Where are you getting this information? I've never seen a bill for an app update (even a $0 bill) and I've not seen any mention of this anywhere else.
Actually, Apple did send out $0 receipts for updates in the early days. I have a few that list for-pay apps as 'Free' because they're updates. But I haven't received one of those in quite some time, so it looks like they've stopped doing it.
Whether they counted those 'sales' towards their billion is another matter.