Technically both. I design them as normal 3D models first, convert them into voxels, and then bake the voxels into a sprite sheet as separate layers going from bottom to top. In game they're then drawn as stacks like a pancake and distorted based on their position from the center of the screen.
This is both an archaic and highly unoptimized method of doing things, but it's also surprisingly easier to do this than using actual 3D models in Game Maker. You can get surprisingly 3D looking things like the gunships and dropship with extra skewing and distortion of the layers.