Are horses faster than water buffalo?
They are. Water buffalo are heavier with shorter legs.
Proably I doubt it, considering how big and bulky buffalo are with the legs that appear a little too short compared to sleek, long legged horses bred and raised for running fast. This is why the native Americans were able to kill more buffalo once they started riding horses. They could catch up to and keep up with buffalo easier.
Prehistoric horses were much smaller. The horses we see today have one toe ( the hoof) and a remnant of another (the chestnut). Horses from that time had multiple toes, and as they evolved, they had less and less toes. To answer your question, that would be no. Horses in these periods are much faster that they were then.