The standard way to do this is to have a 3d box which is large enough in the z direction so that the periodic images don't interact with each other (not much anyway). This distance is different for different systems, but 3 times the x or y dimension is a good place to start. In HOOMD for PPPM it has to be the z direction which is non periodic (either sheet or slab). For the spherical shell, you could try making a box which is bigger than the shell, again making sure it's large enough so that the interactions between the images isn't significant. Ewald based methods like PPPM are inherently 3d, though, and a different method would have to be implemented to be truly 2d.
-Steve Bar