The Washington Post Online has a Home Page Story about Al Queda's maritime activities. It's a fine effort, well worth reading. In my days as a Beltway bandit, I did some work on this issue, working on a computer program to help track ships. The article covers most of the countermeasures that the bad guys can take to escape surveillance.

More than that, there are a number of choke points that most shipping traffic passes through: the Straits of Malacca in Indonesia, for instance. The bad guys don't care so much about time lines, and could send their shipping outside of established lanes. If they were worried about perpetrating attacks at sea, those target-rich environments are well-known.