An AA filter does add a little bit of cost. But you can't remove it and get away with it - the AA filter does two separate things. Besides being a low-pass filter, it is also the protection on top of the extremely fragile sensor.
When people are buying sensor-cleaning kits, they aren't. They are buying AA-cleaning kits. If the camera manufacturers starts to ship cameras without any AA filter that just means that the extra protective glass in front of the sensor should have two smooth surfaces, instead of having one smooth and one frosted side. So no real cost reduction by skipping that AA filter.
And there is yet another aspect too - the sensor doesn't just need AA + mechanical protection. It also needs IR filtering.
If you send the camera in to a company that modifies the camera, then you get to pay for having a clear optical glass fitted instead.
I don't think it's a simple as you make it to be. There are multiple filter elements in both cameras with an AA filter and ones without. It seems to be how the filters behave. Here is a good picture showing the differance between the D800 and D800e.