I went from an Airmar P66 (transom mount) to a B60 (thru hull) on my center console this winter. Both are 600 watts, which suits my primary fishing depths, and comparable transducers minus the mounting type. While stationary, they performed the same. However, I hold the bottom at higher speeds much better with the B60. I lost the bottom very quickly with the P66 once the boat was moving.
In addition, I had some issues with the transom mount last summer-- as in the transducer mount broke in rough water and I lost the entire transducer-- may have just been a fluke, but I like how the thru hull is solidly mounted in the boat. For nearshore/offshore fishing, I would go with the thru hull again without hesitation. However, for shallow water inshore fishing, the transom mount is the way to go since you don't want to be scraping the bottom with your transducer. Also, the thru hulls will give you temperature readings, and the in hull type (shoot through) will not.
There are a couple vendors on THT that are very knowledgeable and will answer all of your questions in regards to transducers. Lots of options out there from inexpensive to very pricey. Personally, I recommend Jim at BOE Marine as he was very good at matching my needs and budget with a transducer.