They can be in the way somewhat depending on your boat setup. I have to raise my motor up to get a great view as opposed to a decent view because of this. Mine is mounted on the right side of the boat. The motor is still far enough in the water that I can safely idle around while scanning. I think some of the newer model transducers may scan more of that horizontal angle but the older ones are angled slightly down so the motor isn't usually that big of an issue. You may want to research your particular transducer that you're thinking about purchasing.
My buddy's boat has enough room that he was able to mount his in the step in front of the prop so it's not an issue at all for his boat setup.