I don't see anything in the screenshot as shadeless black or artifacting. But it does look like basic geometry based shading, so some polygons might end up shaded as if in self-shadow because of how it's triangulated and rasterized. You might want to study how surface shading(in general 3D/CG terms, this isn't specific to godot) works and maybe modify your assets a little to adjust them.
It might even just be that some of them after importing just don't have a material assigned to them so they render with a default placeholder.
