Personally, I insist on receiving invoices before I pay the GST to the Canadian companies that have run our campaigns. I've gone through CRA's standard GST audit twice now and both times I had to provide invoices to prove that I paid the GST for a legitimate reason.
This hasn't been much of an issue with any of my affiliates. Most affiliates doing that volume who've registered as a company almost always have some sort of accounting package.
You're right. I was just speaking from experience about the networks I have worked with. Not all of them request an invoice but you should still have one ready.