At least on the Boeing I fly overriding the AP is a normal feature and will degrade its function to CWS. Our SOPs call for that in a few specific situations but it is not reserved for emergencies at all.
Overriding the AT is possible, that is why there is a clutch in the first place. But it is of course not good practice to fly the whole flight that way. However is good practice to manually override for short term speed deviations. Might be a good idea for example in mountain wave situations.