Yeah, that's what I thought. So regarding the indents, there are really couple ways to go about it. If you really really need the spaceship to be actually destructible as in being able to carve actual holes to the mesh, you might have a long road ahead of you, especially if you wanna do that by manipulating the underlying 3D mesh. Perhaps easier approach would be to use some 3D graphics tricks to make intersections between the two meshes but that too can quickly get complicated and have many edge cases that need to be addressed.
The way bullet holes/impacts are often implemented is via decals. They are like stickers which you can wrap onto any mesh surface. Adding them doesn't actually modify the mesh below them so they are relatively cheap and easy to use (just spawn them at the impact point). If you find good decal textures with normal maps, they can look quite 3 dimensional as if there was actually a whole in there.