So in regards to stud vs bolt in an exhaust you have heat cycling which over time can fatigue the bolt, studs have less of a chance of snapping while torquing the nut and my view is you only get x amount of chances putting a steel bolt into aluminum threads before eventually your stripping the hole. Let's face it the studs and bolts used for an exhaust in our mainstream rigs are not ment for the temperatures they see in our exhausts so failures are possible.
I agree with studs if your constantly taking your exhaust manifold on and off sure but if not and you "prep" and use bolts you'll be just as good. Prepping meaning you are using the right gasket,you use some sort of rtv and you let it cure,you anneal the copper gasket and you apply the right torque with a torque wrench.