I would expect it to be done in flash too. For time-lapse you just need a series of images and basically it's just a fade from one image to another. Looking at this example, I don't think it's a true-time lapse sequence. If you look at the ship that faces us two thirds of the way down - it has another ship berthed right behind. Watch that ship as you move the time lapse control.

As time passes you would expect ships to move and in general things to flit-around as things go about their business. That ship doesn't move, nor does it suddenly dissappear and you can see that the light reflections on the water at night go over the ship as time progressess. If this were true time-lapse photography that wouldn't happen.

In terms of flash this isn't too hard a project to do with a bit of programming.

[edit: if you also look very low down there is a jetty with a smaller boat entering from the open water. In true time-lapse you would see that boat move rather than fade.]