Most of the people who visit this forum have tried multiple methods of mounting transducers with varying degrees of success. The easiest and most common method is using goop. Most of us who have tried that method have learned that over time goop develops air bubbles, (I can't tell you why).
The sonar signals do not pass through air very well so common sense tells me that having the bubbles is not a good thing. I am not aware of any actual studies which prove this to be a fact however.
The other common transducer mount method is what is called the "wet mount". The basic thing that happens when you use this method is that you have a bubble-free liquid connection between the transducer and the hull, (which is about the same density as water and invisible to the sonar signals).
Most people say that this method makes the type of inexpensive fish finders that many of us use, perform better than all the options, (except for when the transducer is mounted on the exterior of the hull as it would be on a regular boat). Until recently most people who wanted to use this method glued a foam ring to the bottom of their yak, filled it with water and set the transducer in the water. This method has issues with the water leaking away or evaporating so the water level has to be monitored.
The newest wet mount method involves creating a permanent wet well that holds the transducer. This well is filled with water and is then sealed to prevent leaks. You can see this method here.
http://www.bigwatersedge.com/bwevb/s...ght=transducer
There is one other method being used by some brave yakfishers. Some brands of fish finders offer a trough-hull transducer option. To use this option, you have to drill a hole in the bottom your yak and then fit the transducer into the hole and seal it in place. I am sure this works great but if the seal fails and you are a couple miles offshore, you could be in for a bad day.
Hopefully this information helps answer some of your questions.
Bob