Nice ...
The S3D is able to export the 3D-Model of any submarine ( open it's .dat file and find point 5 in the list called "Node - NSS [type]", open it and right click on 3d model to export it as an 3d object.
The use something like
http://www.blender.org (it is free) and there import the model again (don't bother trying to open the file, import it). There you can change the 3D Model, save it and import the updated one back via S3D again.
Thanks skwasjer
It is of course much more complicated to keep up with other mods editing the .dat file. Because supermods and whatever like to edit stuff there and you would have to keep adding your own changes to the newest versions to keep up with them if they update their mods.