A lightning-protection system is not designed to prevent a lightning strike, but rather to provide a safe discharge path for the lightning. This is the only viable solution for lightning protection (short of going back to wooden ships, kerosene lamps, and sextants). The technology to prevent lightning strikes does not yet exist.
Lightning-protection systems actually function by acting as the "best" short circuit between the cloud and the water, one designed to lead the lightning harmlessly to ground. The system accomplishes this in two ways: by attracting lightning away from more destructive pathways between cloud and ground, and by sending the charge around, instead of through, what it is protecting.
Surge-protective devices (SPD) or transient voltage surge suppressors (TVSS) should be installed on all equipment that's mission critical, expensive, difficult to replace, and/or prone to lightning damage.
TVSSs are the most exciting development in the field of lightning protection FOR ELECTRONICS.