I think it largely depends on the type of booking. If you merely make a reservation through Travelocity, points will often still be awarded because they are functioning as a travel agent. However, if you purchase a prepaid stay Travelocity is functioning as a consolidator and points typically are not awarded.
Have you had pts awarded on hotel stays booked thru Travelocity / Expedia / Orbitz via the type of "agency bookings" as you described?
The few bookings I made in this fashion have not earned points with various hotel chains.