The good thing about mild steel is it is more forgiving when being heat cycled. If it were stainless, then it would definitely be a problem, especially a thin walled section like alot of the cheap manifolds have.
The common failure point is almost always the heat affected zone, not so much the welded joint. Atleast thats what ive noticed on alot of manifolds that have failed.
So long as its apples for apples comparison then definitely, a properly welded joint will outlast a joint that has defects.