It will probably affect it to some extent. It depends a lot on how you lower it, how much you lower it, and how much you plan to tow.
I used drop leaves in the back of mine. They lower the truck 4 inches, and reduce towing capacity. They are lighter springs than stock, so that is to be expected. I still manage to tow a bass boat with no problems, but I doubt my setup would work for anything much heavier. I do have the option of adding helper bags to the back end for (I think...) $200-$300, but I don't need them yet.
If you lower it 4 inches with shackles and hangers, you'll use your stock springs. They will still have the same capacity, but you'll have less suspension travel unless you notch the frame.
I don't know if notching the frame reduces your abilty to tow a trailer. I can see where it might, since the weight of the trailer is behind the rear wheels, after the spot where you cut and reinforce the frame. I guess the peple who sell the kits could probably best answer that question. You can still add helper bags to that setup as well, as far as I know.
Boatpuller and Jesse Gallegos on this board have a lot more experience with towing with a lowered truck than I do. If they don't come into the thread, you might try sending them PMs.
Slonaker