The Side Imaging pulses cover from the water's surface to past vertical under the transducer. Any horizontal coverage you block with the hull is less horizontal coverage you will have.
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I have not seen any yak scupper recesses that will contain a Side Imaging transducer.
Humminbird Helix 12 CHIRP SI, 1198c SI, 1198c SI, ONIX 10 SI NT, Helix 7 CHIRP SI GPS G2, 360, RC-1