Most are supplied with the transom transducer, but offer a thru hull upgrade in plastic or bronze for between £40 and £120 (maybe more!)
Usually you can glue a transom transducer to the inside of the hull of a GRP boat with only a small loss of range. Experiment by building a plasticine or Blu Tak dam, filling it with water, and putting the transom transducer in. If it works, then stick it on using epoxy or apparently, silicone sealant from the car shop, which would allow you to move the transducer later on.
Doesnt work on wood or sandwich layered hulls though.
My humminbird colour fishfinder is bonded through the hull, (araldite) and works perfectly, although the after sales service from compass24 is the pits,the worst I have ever come accross, and I would not reccomend them to Muslim teddy!
My Garmin fishfinder was supplied with the transom type transducer. On advice from others of this forum, I mounted it inside the hull, sticking it down with silicon sealant. It works well and has registered depths up to 320 feet. My main use for it is to be able to watch the changes in the bottom profile as we run into shallow water so I am not that interested in the fishfinding aspect.
The best spot for sticking it to was found by using wallpaper paste as a coupling medium, as it was easily cleaned off before using the silicon. I just made up about a pint of the stuff and slobbered a handful onto the hull then moved the transducer about over the surface like you see maternity unit staff doing on the stomachs of pregnant women.
My cheapo Eagle fishfinder was supplied with a transom mount but worked fine when held in a shallow puddle of water in the bilge. I tried finding a position with both blu-tak and bathroom sealant as recommended on this forum but could get a signal with neither. I eventually bit the bullet and epoxied it in the bilge and it works fine, with readings down to 100+ metres. The manual contained dire warnings about not cutting the cable, but I seem to have got away with cutting and rejoining it as well.