Are cars which have lowered suspensions more susceptible to getting misaligned due to potholes etc than one which is at a normal ride height?
Yes, considerably more so. The whole point of the suspension it to allow the car to absorb bumps and holes in the road - by lowering it you're reducing it's ability to do so. You're also changing the angles of various parts of the suspension, meaning the forces aren't being transmitted in the direction the manufacturer intended, increasing the likelihood of something bending or breaking.
There's a good reason why vehicles designed for off-road use have much higher suspension!