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.
I have had a thru hull transducer on my Cape Horn 17 since I bought the boat about 8 years ago. As I recall the guy who installed it mounted it with some 5200 or some other adhesive, no drilling involved, it shoots thru the hull. It has been great, I would not go back to the transom mount style. I get very little interference from cavitation even when running at high speed and it seems to be accurate in terms of water depth and fish location. One issue is accuracy when reading water temperature because it is not in direct contact with the water. I find that once the boat is in the water for a while the water temp reading will be more accurate.
You can find detailed info on your particular fishfinder. My kayak setup works fine just using epoxy to mount the transducer inside the hull. It is only shooting through plastic. I know there were some warnings about attempting to shoot through wood. That and the Down Scan Imaging.
FWIW, the worst part of drilling the hole in the bottom of the boat is accepting the fact that you are about to drill a hole in the bottom of the boat... I installed my thru hull this winter in easily under an hour... Very easy to do as long as you have a solid fiberglass vs cored hull.
The fail safe method of installation is to drill the hole and install the transducer. Build a box out of some thin ply that extends above the waterline on the hull. Glass the box. Bring the cable out the top. Fashion a lid and glue, screw, or 4200 on.
It's a sort of a sea chest only you aren't inviting water in like you would be with the sea chest.
All you are doing is insurance. Should you bang the transducer on a trailer or or debris in the water and it starts leaking, the water will only fill the box to the height of the waterline on the boat hull.
A seachest would be building a box and cutting a hole in the hull so the box would stay full of water. Your onboard water raw water needs would be drawn from this box by pump. Sort of a water reservoir, hopefully without trash.
Here is a seachest on a larger boat. We do the same thing on small boats. You aint sucking sand, weeds, and junk. You can also pump while underway because you have a "scoop" on the exterior that directs water into the sea chest.