From my research (not testing, just reading and some conversation with AirMar folks) beam cone angles vary. And even so, I suppose it is possible at shallow depths one might see wrongly-aimed beams still providing useful returns, where they would not do so in deeper water. (Which, if true, might be okay since most of us are not fishing and are primarily concerned with not going aground.)
i believe the instructions I linked give a range of acceptable thicknesses for the glass at the mount point (for one model), as well as explaining that the transducer won't perform when shooting through coring. Also, if one has a single prop, avoid mounting on the side of the boat where the blades are coming up toward the surface, doe to compression waves coming off the prop.
Best advice is probably what was mentioned earlier about testing until you find a location that works.
"I don't have time to get into it, but he went through a lot." -Pulp Fiction