Is the decal shape the same from ship to ship? Is the mesh shape different from ship to ship? Then you'll need to do them by hand. No way around that. Or else, you need to model in the shapes when you make the ship parts.
If the UVs are not heavily distorted in that area you can indeed paint it on directly. If not: - Paint the details on a stencil that you can then project to the lowpoly in a 3d painting environment like Substance painter or 3DCoat, or to the highpoly in Zbrush - Or, create a secondary set of UV especially for decals, and…