Perhaps you missed the part of where the Cutter Revenue Service had the authority to board and search ships at any time. Not much different than the authority TSA has over airplane access at airports.
And perhaps you are unaware that The Customs Department has been rolled into the Customs and Border Protection Agency which is under the Homeland Security Department.
On a Typical Day in Fiscal Year 2009, CBP...
02/16/2010
Processed:
* 989,689 passengers and pedestrians
o 240,407 incoming international air passengers
o 45,735 passengers/crew arriving by ship
o 703,546 incoming land travelers
* 57,761 truck, rail, and sea containers
* 271,278 incoming privately owned vehicles
Executed:
* 2,139 apprehensions at and in between the ports of entry for illegal entry
* 616 refusals of entry at our ports of entry
* 107 arrests of criminals at ports of entry
Intercepted:
* 72 fraudulent documents
Seized:
* 6,643 kilograms of drugs
* $300,582 in undeclared or illicit currency
* 4,291 prohibited plant, meat and animal byproducts, and 454 agricultural pests intercepted
Rescued:
* 488 events with a total of 1281 people
Deployed:
* 21,863 vehicles, 290 aircraft, 225 watercraft, and 280 horse patrols
* 1,419 canine enforcement teams
Protected more than:
* 5,000 miles of border with Canada
* 1,900 miles of border with Mexico
* 95,000 miles of shoreline
Employed approximately:
* 57,519 employees, including:
o 21,058 CBP officers
o 2,394 CBP agriculture specialists
o 20,119 Border Patrol agents
o 1,212 Air and Marine agents including:
+ 47 Air Enforcement officers
+ 823 Air Interdiction agents
+ 342 Marine Interdiction agents
Managed:
* 327 ports of entry within 20 field offices
* 139 Border Patrol stations within 20 Sectors, with 37 permanent checkpoints
http://www.cbp.gov