Just like the 911 airplane hijackers, it is possible, with enough money and some well educated (in how to navigate one of these large ships), to grab a vessel near a major port, or the Straits of Malacca or the Singapore Straits. One of these thousand foot ships could be run into port facilities, or sunk at a choke point and block sea traffic. Such an attack would have a greater global economic impact than the September 11, 2001 attacks. Thats because ships would have to travel several days longer to get to their destination (usually the Persian Gulf, or Japan/South Korea/China/Taiwan). Not only would shipping costs go up, but there would be a lot of shortages, because there is a shipping shortage at the moment. That has been caused mostly by China, which is in the midst of an economic boom that is attracting oil, and raw materials, imports from all over the world.
It is worth re-emphasizing the concern about certain straits and chokepoints. Most of us who drive to work have certain traffic patterns we follow. We try to find the shortest route to our offices. What prevents most of us for driving in a straight line door to door is that there are obstacles in our way. So it is at sea.
The shortest path from Port A to Port B is a straight line drawn on the chart (actually, it's a great circle - but for my purposes here, the straight line concept works). However, ships generally can't sail in a straight line - land masses keep getting in the way. So sailors have to take the shortest practical route which means a series of courses that take their ship around the land, using the gaps between land masses. When these gaps are narrow they are called straits or passages. For our purposes there are a few key international straits. The strait leading in and out of the Arabian Gulf/Persian Gulf (Strait of Hormuz), the strait between the mainland and the islands of Indonesia (Malacca Strait) are two of these. Here are major oil routes:
In some cases, there alternative routes. A ship can avoid the Strait of Malacca but it adds distance and time to the sailing route, and time and distance cost more in fuel and limit the number of trips a ship can make. In a system built on on-time cargo arrival, more ships would be needed to be in the stream to meet the time demands. In addition, even the alternative routes also lead through other straits or passages and these chokepoints can become congested, too.
In some cases, the alternatives to using a strait may be a land route (such is the case with the Strait of Hormuz -there is no other entrance or exit to the Arabian Gulf so if that strait were blocked or otherwise closed, then the only way to get oil out of the area is by a land route, either a pipeline or and huge number of tanker trucks or rail tank cars).
In the open ocean, ships have a great deal of freedom of navigation (meaning they can choose almost any course without running into anything). In straits, however, their sailing freedom is usually limited by the width of the passage and the traffic flow (and in some cases by the laws of the nations who claim "sovereignty" over those passages and who have instituted some form of traffic control scheme. Both the Strait of Hormuz and Malacca have international traffic control systems in place.
In the open ocean, it is much more difficult for pirates to ply their trade. They are far from supplies and have to count on some luck in being able to chase down a ship. As you might guess, straits, being near to shore are where pirates like to work. In a strait, big ships have limited maneuvering room and the pirates can use small, high speed boats in their attacks. Of course, it helps if the strait is a major trade route (even the pirates of the Caribbean did their work on the trade routes). More ships equal more opportunity for thuggish attacks.
All these factors make straits the area of choice for terrorists, too. The chances of success of attacking a large target in the open ocean are low. Put that same ship in restricted waters and the odds go up.
There are some limiting factors. First, a pirate/terrorist's best chances are attacking a undefended and unalert ship far from where help can reach it. Even a ship's crew armed with high power fire hoses can keep small boats at bay under the right conditions. Add in the potential for armed escorts either on the ship or accompanying it, and most pirates will go find easier work. A second factor is that ships simply don't move that fast. Capture a ship at one end to the Malacca Strait and you might have to sail it 600 miles to get to targets at the other end. That might take up to 40 hours. And in 40 hours, a lot of defenses against you can be set up. Try and seize a ship near Singapore (at the narrowest end of the Strait) and you have to contend with the policing efforts of Singapore. Want to take out U.S. carrier? You are going to have to work your way through a number of escorts to get to it. Attack a port facility? Which one? Scuttle a thousand foot long ship? It takes a lot of time to sink a ship that big and what has been sunk can be pumped out and raised if enough money is involved (and in the case of the Strait of Malacca, there's more than enough money). Further, you'd have to sink the ship in exactly the right spot...which is very hard (try dropping a penny in a bathtub and getting it to land in a certain spot...it's difficult).
It is right to be concerned about terrorists, shipping and straits. There are tried and true tactics to help preclude such activity. Post armed ships along the routes to respond to assaults or use convoy operations and escorts for shipping plying these routes. Some of these are being employed now. See here.