You do not get stay/night credits nor points (unless the hotel makes a mistake) if you book via a third-party website like hotels.com. That's clearly stated in the Hilton Honors Terms and Conditions under the Accrual of Points section:
3. A "stay" is defined as the total number of consecutive nights spent at the same hotel, whether or not a guest checks out and checks back in again. Specifically excluded from the definition of "stay" are the following types of ineligible stays:
- third party websites bookings (irrespective of rate paid); and
- "opaque" channel bookings where the brand may or may not be known at the time of purchase.
Source:
http://hiltonhonors3.hilton.com/en/t...rual_of_points
(Looks like Mr. jerry a. laska beat me by a few seconds.)