the stock jeep "header" (actual tube manifold is more proper) is known to crack in the "crotch" where the various tubes join up. most commonly at the final and largest join. most of the aftermarket manifolds use expansion/flex tubes before these joins to help avoid this problem, but it's extremely common to weld the stock ones.
my biggest argument against welding, is that if you can weld it in-place fine ... if you have to remove it to weld it, well then you're already doing all the pain-in-the-ass work, and you've gotta remove the intake manifold, and the shared gasket and everything, so at that point, why not spend $100 to replace it with an aftermarket.
just my 2 cents.