It seems the consensus is that rust is the primary user focused reason to not use a 12 point, and cost being the main reason on the manufacturer side. I must admit I did not consider cost on the manufacturer side. I will have to research a bit on the cost of a 6 point, 12 point, external torx, etc bolts and look into that.
In reference to rust, I can only speak to my own experience and listen to others that speak from experience. I live in Wisconsin, so I experience winter, salt and expect rust on every car I see. The most common issue I run into is the bolt and/or nut being rusted together, rusted into a bushing, etc. In those cases, without care, the bolt heads and/or nut are prone to rounding off with the force needed to attempt removal. I have never personally experienced issues with a 12 point bolt having more issues with rust compared to a 6 point, and the same for external torx. However, I must state that my experience with 12 point and external torx fasteners is FAR less than 6 point, so my experience there is not substantial enough to have meaning.
I posted in other threads on torx and etorx, and my opinion there is that I prefer them due to the extra bite (fastener to socket) I get with them. I believe the same to be true with a 12 point, but my experience is lesser with them. As some have pointed out here, it is true that there are certain tools that cannot be used with a 12 point and an external torx. However, if we are talking about rust, I sure will not be using an adjustable wrench on my fasteners anyway. I do not recall ever using an adjustable wrench on a vehicle anyway. When I have a problem bolt, I pound on a 12 point socket, use a spline drive, try a bolt extractor, etc. When I was younger I used a vice-grip a lot, but in recent years I have found better alternatives that do not cause more damage to the fastener.
I have the opinion, assumption, based on my experience that if the rust here is bad enough to destroy the points on a 12 point fastener, the 6 point will be the same, resulting in a round fastener. However, the 12 point will have more to bite onto, twice the rounded off points. I would be interested to see and hear others experience. I agree that things on paper and hypotheticals are not relevant since we live in reality and not on paper. I am also well aware that other areas experience more rust than where I am. However as some other pointed out with 12 point drive shaft fasteners, I have never experienced issues with 12 point fasteners.