The stock headers are 409 stainless which is one of the lowest grades of stainless out there. It has a very low nickle content and as such is not very tolerant of temperature extremes (which is the reason why stainless was used in the first place)
409 is also prone to rusting much like mild steel.
To properly repair a cracked header, you should Tig weld it and not Mig weld it. The Tig concentrates the heat to the area right around the crack. You will also want to drill a hole at the ends of the crack since the crack could continue even after it is welded.
The header should be scrapped if the pipe is cracked almost all the way around since there is no wayto repair it properly.
Even though the header is repaired is never a guarantee that it wont crack again. If I remember correctly, too much heat in the weld can cause a crack to form at the weld; so be careful!
The best replacement headers would be made out of 304 or even 321. So, if any manufacturers out there are listening, there is a big market for a good stock replacement header.