The problem IS in your textures.
The ship textures must be in dds format dxt 5 with 8 bit alpha. The alpha channel is important, because without it you get "black ship syndrome"
You need an alpha channel in your -cl texture (or "Color" texture) if you plan on using team colors. NOTE: The -cl texture is the ONLY texture that can be used without an alpha channel. No SoA 2 mesh has an alpha channel in their -cl textures.
You need an alpha channel in your -da texture (or "Data" texture) if you plan on using bloom effects. NOTE: If you do not plan on having bloom then the alpha channel must be all black. However the photoshop dds plugin will not let you save an all black alpha. So just paint a white dot somewhere on the alpha channel that wont show on the mesh.
For your problem.. You especially need an alpha channel in you -nm texture (or "Normal Map").
I am not exactly sure why you need the alpha, but i think it has something to do with reflecting the ambient light of the skybox environment cube (this is totally separate from the blue channel reflection in the -da texture). What is important is that without an alpha channel in your normal map you get "black ship syndrome".
The Sins Developers themselves just duplicate the normal maps Red channel, and place it in the Alpha channel (that is the way the dev's told me how to do it). Again i am not exactly sure why, but it works.
Since your ship came from the 3dsmax exporter script, it has NO tangents which means your ship will have some lighting, and smoothing errors in game that can only be fixed by applying tangents to the model in XSI.
Another solution is setting "hasValidTangents" to FALSE. This will make the sins engine simulate a default set of tangents on the mesh, and give it a default 45% smoothing throughout the mesh. It is not recommended to do this, because it makes the sins engine use much more cpu to render your mesh that it would if it had proper tangents (this is also straight from the dev's mouth).
Welding points wont matter since the max exporter doesnt export the smooth data. It is better to weld since its that much less points to calculate. I only separate my master meshes into groups for texturing, and UV mapping.