1) They probably used the fire-beam sexp. That will fire a beam at the specified target regardless of the distance or whether there is a clear line of sight. It also has the benefit of providing the Fredder with precise control over the beams, so if you are Fredding at all, it can be a very useful one to get to know.

2) It is actually pretty easy. There are three main parts to every Freespace ship: the table file information, the model file, and the textures. The table defines things like hitpoints and maximum speed, and references which model file to use. The model contains the geometry data, including references to the names of the texture files to use for different parts of the geometry. So all the Derelict team had to do was replace the textures for the Knossos with new ones that looked Shivan. Because they gave the new textures the same name as the old ones, the model automatically used them instead.
3) In Fred it is possible to change what weapons are assigned to different turrets on a ship. They probably just changed the weapon for an appropriate turret. However, if they did alter the model, all they had to do was to give their new model the same name as the original model and the table file would use it instead of the original.