It is my understanding that a powerful lightning strike to a structure (boat,car, etc..), can create an electrical field often coined EMP, or electro magnetic pulse. Think of it as a cloud of high electrical energy or charged atmosphere, separate from the actual bolt itself. This EMP can invade electronic devices, and whether plugged in or not, they can be destroyed as the energy finds its way into delicate circuitry such as transistors IC's, and microprocessors.
Further, it is my understanding that gounding these devices internal chassis grounds to the bonded and grounded structure, will either help to disipate the EMP energy away from the devices, or not allow the EMP energy to build in the first place.
In aviation, aircraft are struck by lightning almost every day, and often multiple aircraft every day. Consider that these aircraft are primarily aluminum structures and highly conductive. Consider also, that all electrical systems and equipment aboard are thoroughly grounded to the chassis, and all parts of the chassis are bonded electrically to each other. The aircraft's body, or fuselage, becomes a faraday cage, and as long as all electrical grounds are connected to that chassis, the energy stays outside.
In a strike, the voltage passes over the outside of the aircraft, and most often without any physical damage whatsoever. It should be of interest, that the Apollo 12 spacecraft was struck not once, but possibly multiple times, during liftoff, when the exhaust plume created a pathway for energy of nearby storms during launch. It knocked their computers offline but they were able to reboot them and continue on to the moon without trouble. I can assure everyone, that the ships entire structure and electrical components and systems were completely bonded and grounded.
Our boats are wood and fiberglass and not highly conductive. By bonding all conductive metallic hardware together and installing ground plates below the water line, we are recreating the aircraft chassis. It is my understanding, that electrical systems not directly connected to the bonded and grounded structure, create a potential source of increasing the EMP energy, and a pathway that could potentially pull the EMP energy "inside" the cage.
From what I have garnered, it is advisable to either bond and ground all it fully, or do nothing at all. But dont do it halfway. You may invite far more damage than either process.