Transom mount are the most sensitive. You loose sensitivity and range going through the hull. On a wakeboat application, unless it is installed far to the edge of the boat, the prop wash will affect your sensitivity as well.
From what I have seen, In hulls are old school and no used much anymore, at least in smaller boat applications
Thru hulls are the easiest to install and mounting it in front or right near the vdrive will be optimum position. Don't run the wires near other wires or electronics. Some transom mount transducers can be installed as a thru hull transducer with marine epoxy. If your only worried about depth, thru hull will be just fine.
If your boat has a depthfinder in it already, compare the frequencies of each unit. There may be some interference when you install the new one.