I'm guessing you're importing 3D objects into Unity, then using a shader for the pixelart effect. Is that right?
its slightly more complicated then that
im rendering the world at a lower resolution outputing it to a render texture, snapping the camera and sprites so that they move by a pixel increments in world space.(if you didnt snap them they would look more like low res 3d objects rather than 2d sprites with the abillity to cast shadows and recieve lights)