Longtubes are less hassle to get hooked up and are a direct bolt on unlike shorties. I would definitely stay with LT's if you can despite any if little gains.
But in cali you have to run shorties an I heard jba shorties were carb certified but could be rumor. Lt's are a no no in cali unless you know someone or you change them out everytime you gotta do emissions.
I'll answer for Jeff, although the shorties are carb legal, you have to use the stock 600 cell cats. They are much more restrictive. If you're not in Cali, then go with the LTs