Hi, slavik. What leads you to believe the Powerbook is overheating? Is it going to sleep while you use it? Shutting down unexpectedly? Misbehaving in other ways? If the temperature sensing and fan control system is working properly, the PB should go to sleep before it gets hot enough for serious damage to be done. If those systems aren't working properly, it might really overheat, and then other misbehaviors would probably appear.
I don't know for certain, but I assume there should be no voltage at the fan contacts unless the temperature sensors in the Powerbook detect excess heat that needs to be removed — that is, I suspect there should be no voltage to the fan when the Powerbook is running at an acceptable temperature. There is no published documentation of the temperature at which the fan should come on, or where — at which sensor(s) — that temperature must be reached to trigger the fan. You've already determined that your fan works when you give it power, so I can think of only two possible explanations for its not running in the Powerbook: either the PB isn't hot enough for the sensors to turn the fan on, or the sensor and fan control system isn't working properly. In the former case, there's no problem at all, and in the latter, the logic board probably needs to be replaced, since that's where most of the sensors and the control system are located.