We're Americans, dammit. We're not supposed to be afraid to do anything. That's why this place is supposed to be better than Pisswater, Central America.
This is one more reason alright. A reason to get real angry come election day.
Barring that, its a good reason to point your boat at the horizon and not look back.
We did that in 1994,2000, 2002, and 2004. Things got worse, not better.
If you're docked in a port connected to an ocean, or any large navigable waterway they have the authority and the legal right to do this.
It's not anything new. Hell, the Coast Guard can search US Flagged vessels outside the territorial limits on the high seas.
I do wish they weren't sniffing around pleasure craft in Monterey Bay and instead concentrated on actual threats to national security but the fact remains they've had the power to do so for longer than I have been alive, and that's a while.