Agoda is a subsidiary of
Booking Holdings as are Booking.com, Priceline.com, Rentalcars.com, Kayak, OpenTable, Rocketmiles, FareHarbor, HotelsCombined, Cheapflights, momondo and Mundi, and probably a few others.
I usually book hotels through the American Airlines AAdvantage Hotels portal (it all about Loyalty Points and oneworld Emerald status for me). Often, when I check-in or get my receipt at the end of my stay, it shows that the booking was made by an online travel agency with which I had never dealt; sometimes, it is one of the entities that I have listed above.
I suspect that Booking Holdings, books and prepays for blocks of rooms that they later resell at a profit though one of more of their subsidiaries.