You could do it like this:
1. Use a 3- or 4-wire fan. Connect it to the Duet as described on the Duet3D wiki. For Duet 2 you need to connect the tacho wire to the Duet via a diode. Duet 3 and 3 mini support a direct connection.
2. Configure RepRapFirmware 3 to use the tacho wire and display the reading in the web interface.
3. The tacho RPM reading and hot end temperature are both available in the object model. So in the daemon.g file you can use a loop that checks whether the hot end is hot and the fan RPM is too low, and does an emergency stop if so.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].