Most (but not all) martial artish NNDs will have predetermined hit locations. If sucessfull, they will always trike the specified location, but receive no modification (good or bad) from that location. Examples include Choke Hold (neck), Nerve Strike (usually the vitals, sometimes neck), Ear Slap (well, duh). Others affect something beyond the simple physiology of the character (a ch'i attack for instance) or something internal (like a poison) and the hit location, though it can vary, won't make a bit if difference.
Now if you want to get creative, you can say a Nerve Strike will have different effects upon striking different parts of the body. After all, not all nerve centers are created equally. In this case, rolling for hit location, as using called shots, would definately apply.