According to Rob Galbraith, Canon and Nikon camera indeed either read or interpret color temperature and white balance from the preflash, and adjust the camera accordingly.
I don't want to claim more knowledge, but I did research this a bit.
By definition, pre-flashes happen before the shutter opens, so in order for a camera to be able to see color without using its main sensor, it must have a color sensor somewhere else. I have found that in higher end Nikons, the 3Dmatrix meter sensor is also sensitive to color, and is used to help calculate white balance separate from the main sensor. Also, some of the Nikons have a white dome over the prism that meters the ambient light, and this measurement is added to the calculation.
For the Nikon system, it seems that any digital era speedlite, including pop up flashes, will be used for this metering proceedure. I would expect a speedlite does not NEED to be in the hotshoe, as long as the camera knows it is communicating (i.e. the CLS system). Also, some newer Nikon speedlites come with flash gels which are coded (kind of like a bar code or DX-code) that tell the flash and camera what type of gel the flash has on it. On these cameras, the gel code, ambient light, preflash, and information gained from the actual image sensor upon exposure are used to calculate white balance.
I do not think all Nikons use this system and I did not specifically see any information about a similar Canon system , but I would not be surprised if one existed. Without this system in place, the preflash would just be used to calculate flash exposure, and a camera would base its white balance on information gathered during exposure, and the fact a flash was attached. Logically, the color temperature of the flash should be calculable based on the output. I would not be surprised if some systems account for that.
Again, a speedlite would not necessarily be in the hotshoe, but would need to be recognized by the camera. Flashes triggered by a basic radio remote or optical slave would not impact the camera in the same way.
It also seems the system for calculating AWB evolves over time, so that one camera/flash combination my act different than any other combination. This can change even with a firmware revision of the camera or flash.