How neodymium magnet affect (if any) on extruder motor
The best way to know is placing the magnet on the shaft; if you see that motor starts shaking or stops this mean that you affects the motor operation, but I think if any magnet interference can be deprecated due internal coils of the motor during operation. 

The motor works with some coils in the rotor and some magnets in the stator (motor frame). But the shaft is to far from the coils to be affected for the magnetism of one small neodimiun magnet which needs at least 7mm to trap another small metal objet or for induction sensing and 2mm as maximum for creating electrical flows (generation); this values are afected if the magnet is placed over other metal part reducing his atraction field, and the armor is too big for an small magnet 8x3mm.

You can attach some indicator with a double sided adhesive tape (3M) if still are worried about affecting your extruder.

If your motor extruder is heating during extended usage periods you should adjust the motor current, for example: you motors is rated 0.5A you should calibarte the current for 0.48A or 0.45; this could reduce the torque force of the motor by a little. Or maybe the current current :D is calibrated above 0.5A thats way you are getting over heating.