an aftermarket kit will be a larger diamater (at least 4") which is significantly larger than the stock pipes (usually 3"-3.5"). also the bends in an aftermarket kit are a little more free flowing than stock exhaust. if you want performance upgrades, an aftermarket kit would be better because the exhaust gases would be more free flowing. you would still have sound with the deletes, but you would have more sound with the aftermarket kit.
i had a 4" dual straight pipe kit on my 2000 f350 7.3 and it sounded BEAUTIFUL with very little cab noise. FYI, i bought the kit on ebay for $399 and it worked great. cant remember what brand though