The DRV8825's have protection diodes built in to their H-bridges, and they are actually using the BEMF currents as part of the motor current regulation circuitry. No external diodes are required (
see here).
It's not a particularly good idea to manually slew the scope with the motors connected, but in practice it shouldn't matter. You have to remember that the gear ratio between the motors and the worm screw are usually very low (~5:1) in which case the motor doesn't spin all that fast and the built in protection circuitry should have no problem coping. For the Skywatcher motors, the ration is very high (~120:1), and it's actually almost impossible to rotate the output shaft manually which is why they come with clutches for disconnecting the gearbox when doing manual movements.
The other thing to note is that there are plenty of decoupling capacitors of the motor driver supply pins in the AstroEQ design. This is done specifically to make sure if there are any back EMF spikes, they are quickly absorbed.
That's not to say its impossible to get spikes which cause problems - in fact very rarely if you unplug the motors while still powered (definitely not recommended), it has been known to reset the microcontroller.
