I think the key is whether or not the booking is completed at the airline / hotel website.
I know for a fact that for Delta & United - bookings completed there as redirected by Ebates (ebates for DL is 2%) or Mypoints is eligible for miles.
For hotels - I don't think that Hyatt participates directly at any portal any longer. Bookings completed at any third party site renders the stay ineligible for points / stay credit. I believe it is the same for the other hotel companies.