That makes total sense. They absolutely would not stop any mud. The fact that Subaru even charges extra for those is ridiculous - I know all manufacturers count those as accessories. The price should be no more than $20/pair.
I agree the splash guards aren't going to stop much mud, but they are an improvement over not having them installed. Like mentioned earlier, if they extended further down, ground clearance claims would likely be affected. For the minority of people that will need added protection over what the splash guards provide, the aftermarket (Rally Armor, RokBlokz) will surely have more robust offerings in the near future.
As far as the cost, Subaru has to be able to get a return on investment on these. $20 / pair would not come close to paying for the injection molding tool for those parts.
Although in my opinion, Subaru would be better off having the splash guards standard and no other option.