You have a loose or missing ground.

Under the dash look up and you will see 2 buss bars 1 for power 1 for ground. The noise sounds like the system is grounding through the horn and creatng a light hum alarm sound. The horn could even be shorted from water (I doubt that though). The horn sits in front of the sub wall under the dash on the starboard side. It would easily echo down that wall. Also check the buss bars by you amp under the port locker. Check the starter connections and engine ground strap.

Even though you treat your boat like a baby (self included) I have found loose screws and bolts all the time. That JL amp is nice and is going into protection because it doesn't have proper ground. Engine speed causes the vibration wire looses strong ground goes into protection.