My last two stays have earned stay credit and points. Many posters have stated that they do. If you search for blog posts you'll see the same.

You don't even need to contact the hotel - can input HHonors number at time of booking. Booking will appear under your reservations list.

I'm guessing it's like an authorised Travel Agency of some sort; the rates given are typically identical to what's on the Hilton website. Given that Visa seems to be a partner of some sort (based on the various promotions available) I won't be surprised if that's the case.

Can't say about other chains, though...