Animating a shape layer with the pen tool is the same for 3D layers as it is for 2D. One problem is that if you're moving paths around on a layer that is not parallel with the view then you have pespective issues, or parts of your layer might go out of view.
To get around this you can create a new camera that is parented to the shape layer - best to do this before transforming the shape layer. Then you can switch to that camera to get a straight-on view of the shape layer.
Here we have the shape layer with animated paths and a camera called "shape cam" that is parented to it, as well as the scene camera called "active cam".
If we switch to shape cam using the viewport control at the bottom of the comp window we see a flat-on view of the shape layer, for easy editing. A handy tip is that once you've switched from one view to another, to switch back to your original view you just hit escape, so you can toggle back and forth with ease.
You can also set up another view (view > new viewer) and lock one on the shapeCam (the padlock in the view tab) and one on your scene camera, so you can edit your shape layer in one view in mock-2d and see it from your 3D camera at the same time. Here we see the shape layer at the next keyframe, where the paths have been edited, from both the shape cam view and the scene camera view.
An advantage of using shape layers is that they are not raster layers like an adjustment layer with the stroke effect. You can zoom right in on them without the pixels ever getting nasty