You can mix 2D and 3D in Godot freely. Unlike other engines, Godot allows you to combine every engine feature together. That said, the 2D and 3D are separate rendering (2D is not fake 3D) but they can be composited easier. You can see the API here, on how to draw lines and arcs and stuff.
https://docs.godotengine.org/en/stable/tutorials/2d/custom_drawing_in_2d.html
This is for 2D, but the same code would work. You would just have a 2D layer over the 3D game. Then you can convert a 3D point into 2D screen space. You can do this with the function unproject_position() on the camera.
https://docs.godotengine.org/en/stable/classes/class_camera.html#class-camera-method-unproject-position
Then draw just like normal. I think any CanvasItem can be drawn onto, so you could make an empty Node2D to do the lines. However, if you need 3D objects like ships or planets to clip and interact with the lines (not just a 2D overlay) then you will need to use the 3D drawing features. These are not as robust as the 2D, but should be good enough if you work with it for a bit. However, 2D will always look better, I know there are some issues with stuff like anti-aliasing and uniform line width when drawing in 3D. But it is possible.
Here is a tutorial for drawing in 3D, it is much more complicated, so I would try the 2D version first to get it working, and convert it to 3D later if necessary.
https://kidscancode.org/godot_recipes/3d/debug_overlay/
