It is kind of strange that online shops are in with this. I mean the links are there anyway, there is no additional benefit for the shops but they still have to pay additional costs in that way.
My best answer is that right now, they realize it's best not to ruin a great thing. They're on top of the world, things are going well, why rock the boat?
MercadoLibre, one of the biggest ecommerce platform in latam, had an affiliate program, but they cut it when they were "big enough".
I guess it might make sense to view this as some sort of avoided opportunity cost: reddit could potentially redirect existing product links (say, to a CPU at Newegg) to a different shop.
My guess is that they kind of have to because they have an agreement with the 3rd party that's handling this.