In Nikon D90 there are three options for the flash units (for both master and slave) in commander mode: TTL, M, and -- (there is one additional for slave).
In the double dash mode, the master flash fires only for triggering the slave unit and it does NOT contribute towards exposure. However, if you set the master flash to TTL mode or manual mode then it will contribute towards exposure.
See the attached pictures for comparison. The slave flash was kept on the right side of the box. In the first pic, the master flash (the popup one) was set to TTL and it did fire. In the second pic, it was set to -- and it did fire only for triggering the slave but as you can see that it did not contribute towards exposure.
Could I ask you to repeat that experiment with a reflective surface?
So fire using "--" at an item that is placed infront of a shiny surface such as plexi-glass/acrylic/mirror/glass ... I think you'll see slightly different results. My experience has been that in almost all conditions when set to "--" the pop-flash doesn't show up (effect exposure), but when shooting glass against plexiglass/acrylic, you do tend to end up with reflections of the on-camera flash.
I did the experiment suggested by Vikram. The most reflective surface I could find was my iMac's screen. The slave flash unit was kept on the right side of the screen. Here are the results:
Pic 1: Popup flash set to off (--): You can see in the first pic that the popup flash did fire and contributed to exposure.
Pic 2: Popup flash set to off (--) and blocked by a black sheet: You can see that the only flash contributing to the exposure is the slave one.
Pic 3: Popup flash set to TTL: Both popup and slave are contributing to the exposure.
Pic 4: Flash off. Just to show you guys that my mac isn't as ugly and dirty as it appeared because of flash in first 3 pics
Vikram, you were correct, reflection of the popup flash is clearly visible in pic 1.
Thank you all for contributing to the discussion.