Unfortunately, this isn't terribly different from the experiences some of my friends have had with US Customs, when returning from sailing trips in the Caribbean. Searches that actually damage boat fittings have occurred; upholstery opened up, etc.
I'm curious about the circumstances of these inspections. Presumably they were not departing to/returning from seaports, but to/from private marinas. How would US Customs have known of their exiting/return to US territory? Is it possible these were Coast Guard inspections and not Customs inspections?