Applying Blender's freestyle

I am currently working on a project that I think blender can help with. I am a maritime archaeologist who works mostly with underwater sites. These sites can be anywhere for just a few feet to several hundred feet below the surface. One of the most important part of an archaeologist is documenting sites. We often us photogrammetry to do this. Sometimes, like with the deep sites, all we have are the 3D models that are produced with the photogrammetry. Although the 3D models look great, we can’t really analyze the models them self. What we do is make 2D artifact drawings, like a blueprint, from orthographic images that are generated from the models and analyze those. You are probably wondering what this has to do with blend. Well the project I am working on is automating the 3D to 2D process. Currently we trace the images on the computer by hand. This can take some time, especially when the model is of an entire site (excavation, shipwreck, or submerged landscape). I have been looking at blender because of the freestyle feature. I have watched the tutorials you have on freestyle, but they are a little outdated and I need a bit more in-depth help. I think I may have a bit better luck with scripting the freestyle in python but would like a bit more help before I attempt that. Another thing is that since these models are created through photogrammetry they are not as clean cut as ones that are generated by a user. The models can be a bit choppy. Even when laser scanning real life objects the models are not completely smooth. I still need to keep the integrity of the models as the dimensions are the main reason, I am converting them to 2D images. There is some leeway though in how exact they are. So, creating a less choppy model is fine and would help with the end results of freestyle. When I have added modifiers to attempt this though I get holes thought out the model. It seems as if each triangle of the mesh shrinks individually disconnecting them from their neighbors. I am not sure how to fix this. Any help with this would really be appreciated.