Ah, lets think about this for a minute. If, as Elevatorman says, "Towing capacity is based on vehicle weight,brakes,and overall ability to pull and stop safely," then I'd say a suspension lift could have an adverse effect, at least to a small degree.
With the lift comes a higher center of gravity so already stock handling has been altered. Then along with a lift usually comes larger tires and/or wheels which means more unsprung mass for the OEM brakes to stop. As most of us would attest that have gone this route braking efficiency can suffer anywhere from mild to moderate depending on the condition of the existing brake system and rest of the vehicle.
And what else has been done to compliment that lift? Body armor? More skid protection? Heavier bumpers? A winch? All of which will cause further degradation to factory braking ability.
So, in my mind at least, it would behoove anyone that has modified their rig in any of the manners listed above to also invest in upgrading their stock brakes as well. I'm an EBC brake pad and rotor fan but then I also hear there is another pad available, Black Magic from Savvy Off Road, that has shown outstanding performance. Of course, if you have the cash there are complete system offerings from Vanco (my preference) or TeraFlex, and probably others as well. Additionally, or as an alternative route would be to have a trailer with electric brakes.
Now if you don't tow often or far, maybe this all seems like overkill to you and I know we've all heard stories of guys that have towed 250 foot luxury yachts across country during white-out, blizzard conditions without incident but I like to think differently and while I hope for the best, I plan for the worst.