This is a poorly educated guess, but I would suspect people running online chess sites are interested in having as few cheaters as possible and it sounds reasonably trivial to randomly sample games and check what the winner did against the top move choices of the most popular engines and if you find a suspiciously well played game by someone, you check the other games of that someone.
Still, someone determined to cheat could probably fool the system by injecting inaccuracies here and there, by using several different engines and by identifying and not playing the most inhuman moves (since computers have no sense of aesthetic and a very deep view of the game, it's not uncommon their top moves are exceedingly bizarre and obscure and basically unplayable by humans because they look or feel wrong). The paradox here is that you need to be so good at chess to be able to cheat undetected that you probably don't need to cheat nor see the interest of it in the first place!