Usually, in these cases you could add your Bonvoy number at check-in or by e-mailing the hotel; however, in most cases you would only get points only for extras such as meals, parking, minibar purchases, Wi-Fi, etc... spent in the hotel.

In a relative's recent experience, he booked through Hotels.com, did get his free Wi-Fi benefit and points for parking, and meals ( including the hotel restaurant and the on-site Starbucks at the hotel ). However, no status nights or points for the room base fare.