Lots of threads on Headers, but how about one more quick one!
The fender well headers have pretty significant wheel/tire and ground clearance limitations. You end up with some pretty skinny front tires to clear the pipes. Kind of an old school drag race item.
And cutting the fender wells out definitely has chassis strength implications. It depends on how much metal you take out of course, but if you take a look at the US Cartool inner fender braces you can see they think there's a reason to strengthen that area further, not cut holes in it.