For the record, you can set the popup flash not to fire and still control off camera flashes. I did this for a photo shoot of a cabin up in North Carolina last November.
No, it still fires even if it's set to be used only as the controller. The way it controls the off-camera flashes is by emitting short flash bursts that act as control pulses; the spacing and timing of the control pulses transmits the info to the off-camera units.
The pre-exposure control pulses are sent just before the camera shutter opens, so have no effect on the exposure. But the pulses that tell the off-camera units to terminate their output happen while the shutter is open; there's no way to avoid that, because the shutter has to be open while the off-camera units are firing, and it's the termination pulse that tells them to stop firing.
Super-crude ASCII representation of what's happening:
******************************************[open]
Camera shutter: ---------| |------------
Remote units: _______/---------------\__________
Commander: ____^^___________^____________
[start] [stop]
The control pulses are very short and very low in power, so it's true you won't notice them in most moderate-aperture, medium-distance shooting. But if you're shooting at wide apertures and close distances, the control pulses can still contribute enough to the exposure to be visible.
But don't take my word for it; prove it to yourself. Set up a shot with remote flashes and your on-camera flash set to commander-only mode. Include a mirror in the scene, angled so the camera will be visible in the shot. (Don't have the camera pointing
straight into the mirror or it'll throw off your exposure.) Then take the shot and look at the result. You'll see the on-camera flash is firing during the exposure; what's showing up in the picture is the control pulse that tells the off-camera units to stop firing.
Incidentally, don't blame Nikon for this; all manufacturers' off-camera TTL systems work the same way, via control pulses emitted from the commander unit. (If I recall correctly, Minolta invented this concept and Olympus, under license, was the first to use it in a camera system.)
The SU-800 works exactly the same way; the only difference is that it's got an IR filter over its flash tube so it doesn't emit visible light. As Chris said, putting an IR filter over the built-in flash does the same thing. The remote units are IR-filtered (that's the dark plastic lens over the sensor "eye") so there will be little or no effect on range.
Old trick: If you've still got a box of Kodachrome slides somewhere with the black leader still stuck in the box (labs used to include the cut-off leader in case there were partial exposures on it) the black piece makes a pretty good IR filter; Kodachrome dyes were formulated to stop visible light but pass infrared, so they wouldn't heat up as quickly in the projector.
