Hi Wotan_100, welcome to the forums. Well right now the SSE CCC (Content Creation Contest) Is going on, and members of the SSE community are competing who can design the best 3D model for SSE. You can find the entries in the SSE forum called CCC. Whoever wins will get thier model put in SSE. A program that you can build a 3D boat would be Google Sketchup. I would say it is the most user friendly and popular, there is a free version and a Pro version.
But that is for Ship Simulator Extremes (SSE)
For Ship Sim 2008, I doubt more ships in the shipyard will be added since the new release of SSE.
Hope it helps