I used to have a Mk 2 jazz and am a regular user of Isle of Wight ferries.
My alarm on the Jazz, and my Civic have never gone off no matter how choppy the sea is.
Mk 2 Jazz only had a perimeter alarm, which means entry via doors , tailgate or bonnet will set the alarm off, my Civic is the same.
The alarms that go off on ferries are one with a movement sensor- I don't think the Mk 3 Jazz has this, and you can check by rocking the car/kicking tyres with the alarm set. If it doesn't go off it will be OK on the ferry.