Customs/terrorism:
One essential difference between GA and small boats is the speed of movement from one area to another. Both customs and counter terrorism rely heavily on intelligence and this needs time to respond.
If suspicious activity is seen around an aeroplane which can be in another country in less than an hour, the security forces have to move quickly. If they know where it is going, finding and following it is much easier.
Even a good power boat would give them several hours to react. An average yacht could take over 12 hours for the same trip.