Here's a rough overview of rates that travel agents can book:
1) published rates / GDS rates (e.g. "Best Available Rate", advance purchase rate, senior's rate, promotional rates offered by the hotel etc.)
2) consortia and similar rates (e.g. AMEX FHR, Virtuoso, Travel Leaders Select etc.)
3) OTA rates (e.g. booking.com, expedia.com etc.)
4) unpublished (discounted) rates (especially pre-paid and/or non-refundable)
Bookings made via a TA using rate types
#1 and
#2 most definitely qualify for stay/points credit.
#3 generally don't (same as if you made a booking yourself on booking.com or expedia.com) Same usually applies to
#4 , that there are a plethora of different types of rates and giving a blanket answer is more difficult.