It's up to you. Either approach is ok, depending on how your wire run is laid out. If you have the ability to run it through the engine wire chase that's probably your best option, the less holes the better. The important part is to ALWAYS create the transducer hole (if you're making a new one) above the waterline.
Also, you'll want to make sure that the wire is secured from the transducer mounting point to the hull penetration. Weld Mount wire tie bases are great for this, as they do not require you to drill into the transom to secure the bases.