Is there a reason not to use studs that are threaded all the way through?
I am not a mechanic by education. I have learned what I know about engines by doing it and asking a lot of questions.
I found this image of 4 cylinder block with studs exposed.
Thinking about your question, I was taken down the rabbit hole of stud fasteners and why they are used.
My first thoughts were about strength. The threaded portion of a stud has material removed, making the fastener's core diameter smaller. My thinking: The process of creating the threads reduces the strength of the stud.
Then I came across this discussion.
In terms of function, the use of studs provides much more accurate and consistent torque loading. When a bolt is installed, the act of tightening results in both twisting (torsional load) and stretching (vertical, or axial load). This results in the bolt being exposed to two forces at the same time, as well as experiencing frictional loads at the thread engagement. When the nut is tightened on a stud, the stud stretches on its vertical axis only. The exposed end (top) of the stud features “fine” threads, which allow more precise and therefore accurate, torque readings when the nut is torqued (or torque/angle tightened) to spec. by Mike Mavrigian
If the purpose of the fastener is to accurately locate the engine head and provide consistent torque loading of the head to the engine block, then a stud with a smooth middle would be the preferred choice.