ANY engine will benefit from exhaust headers to some degree - if you look at the stock manifold on any tundra you'll see that the center 2 cylinders exhaust into a brick wall of pipe. This arrangement will cause exhaust pulses to bleed into the neighboring cylinders next in firing sequence working against the volumetric efficiency of it's combustion cycle. Anyone that has messed around with muscle cars will tell you that the use of a header, if carefully selected, will greatly improve overall engine performance throughout the rpm range. The dyno numbers may not reflect the performance gains, but you'll feel the difference in part throttle performance where most everyday driving is done.There's a lot of information on the board about this topic.
In a nutshell, conventional wisdom seems to be that the '05 and '06 vvti motors do not benefit from headers or other mods like cold air intakes.