DrDiettrich:
How do you control the fans, using PWM or what else? Does the controller have enough pins for that purpose?A multiplexer won't help, as long as you risk to loose hall effect signals from the fans. But you can try to poll these signals, instead of using interrupts.
For controlling the speed I`m using a Digital potentiometer. And with the Interrupts i would count the number of activations of the sensor(s) in a defined time.
I would connect the Hall efect Sensor to the multiplexers the same way as it is connected in this picture to the arduino And i would like to use the interrupts because of the better accuracy.