The stainless steel is tough, but it is also brittle, meaning breakage is more likely. Its toughness would make it harder to drill out should it break. SS can also have galvanic reactions with other metals, namely other stainless surfaces and aluminum. This can mean that seized fasteners might be more likely, even guaranteed. Due to the heat and location of the manifolds, stainless steel is not needed. A good hardened carbon steel bolt will do well. Studs are better because they have more than one way to come off should one end seize. The best insurance against seizing is to remove the fasteners when everything is cold, and to soak 12 hours earlier with PB Blaster.

I just recently removed an exhaust manifold on a '97 4.0L, all fasteners came out easily and smoothly. I used the PB Blaster beforehand. Impact wrenches on lower torque settings can also be useful, impact tends to loosen things up without breaking stuff.

If you do use stainless, research the types of fasteners to use. Not all stainless is equal.