As far as I can see, this still hasn't been confirmed yet.
Perhaps not confirmed, but come on, deleting stored Pokemon cause the fee wasn't paid would be the biggest of dick moves. I could be wrong, but since I'm sure Nintendo doesn't want to deal with people raging that their Pokemon uploaded to the servers were deleted because they couldn't pay (this also applies to those uploaded during the free trial), they'll just prevent you from accessing them. They'll be there, safe and sound, but you won't be able to access them, I'm sure.