The current generation of fish finder systems are getting more sophisticated every day. Transducers are becoming larger and more sensitive. There is also considerable change in technologies with current generation trolling motors. Models such as Terrova, Xi5 and iPilot do not easily allow mounting of transducers.
However, the one thing that is not changing, is the ability of a trolling motor to pinch, rip, stretch, and generally ruin a transducer cable. For example, if you are able to mount a transducer with Xi5, it will either catch the cable in the mechanism, tearing it or potentially spin until the conductors rip. A transducer on trolling motor is just a bad idea!
In addition, the quick movements of a trolling motor mounted transducer tend to ruin imaging from these expensive units. While the image will be eventually be reestablished, a ruined cable will cost you several hundred dollars.
In order to obtain maximum performance from a bow mount transducer, it is extremely beneficial to separate the transducer from the trolling motor. This helps to improve image quality and will also help lower the potential for electrical interference.