Having just been through the same dilemma/question, it basically boils down to "can the through hull be mounted so that it can see both sides of the hull line"
That is dependent on 2 things, the deadrise of your hull and the mounting block supplied with the transducer. There's a diagram in the installation instructions that, if you read it about 200 times, finally makes sense.
I posted some photo's of the install on a 20' CC in a thread "998 & Thru Hull", not quite the same thing but perhaps enough to give you an idea.