Navy SEALs Inspecting Radioactive Ship Off New Jersey -
http://www.foxnews.com/story/2002/09/12/navy-seals-inspectin...On Tuesday November 3, a special Israel Navy force intercepted and boarded the cargo ship "Francop". Some 500 tons of weapons, rockets, and missiles were uncovered aboard the vessel, disguised as civilian cargo and hidden among hundreds of other containers. - http://mfa.gov.il/MFA/ForeignPolicy/Terrorism/Palestinian/Pa...
Greece intercepts mystery ship with 20,000 Kalashnikovs onboard - http://rt.com/news/greek-seize-ship-kalashnikov-503/
The Israeli navy released Monday afternoon the HMS Beethoven, a Liberian-flagged German vessel it apprehended 160 miles off the Israeli coast, on Sunday afternoon, on suspicion that it was carrying weapons headed to Gaza. Thorough overnight inspections of the cargo turned up nothing problematic, and the troops let the ship continue on its way. - http://www.timesofisrael.com/navy-releases-liberian-cargo-sh...
In January the amphibious transport USS San Antonio stopped a Russian-owned cargo ship, the Monchegorsk, in the Red Sea. US intelligence had received a tip that the freighter was carrying weapons exports from Iran – a violation of United Nations sanctions. A US Navy boarding party confirmed the presence of arms. ... As this incident shows, the US Navy and allies have ample experience at interdicting suspect vessels on the high seas. - http://www.csmonitor.com/USA/Military/2009/0624/p02s04-usmi....
So you are right, these are not "just to have a look around." They are being stopped for a reason. Also, these couldn't wait until the ship got into port. In the first case, the ship might have had a nuclear bomb.
And I think the coast guards and navies want to continue to be able to stop ships at sea in the future and inspect cargo.
Also, the GPS wouldn't be 100ft behind the ship. The antenna needs to be above the surface, which means there would need to be a (visible) cable pull it along, and there would be an extra wake.