Some hotels will still provide status benefits even when booking through a 3rd party site (like BA), even though the HH terms and conditions are clear that hotels do not have to provide those benefits. Others follow the t and c's.
See these threads:
http://www.flyertalk.com/forum/hilto...ed-hilton.html
http://www.flyertalk.com/forum/hilto...n-website.html
http://www.flyertalk.com/forum/hilto...s-account.html
http://www.flyertalk.com/forum/hilto...m-booking.html
http://www.flyertalk.com/forum/hilto...-benefits.html
http://www.flyertalk.com/forum/hilto...-bookings.html