Shorties, long, big difference??

I had my sites set on a pair of hooker comp headers for my 468, with 3inch exhaust all the way bak, still not sure on the mufflers yet. I am thinking now though, that the car will be lowerd 2 or 3 inches all around, so i feel full length headers may be to low under the car, is there a differnce in what sizes should be used if i am to use shorties instead of full length headers? Thanks..Josh