Why not make an applique cupcake design as a patch and mount it on the card using foam pads to give a 3D effect?

I agree with the patch idea from Sue, as I haven't seen any cupcakes that weren't so dense so as not to perforate your card stock.

I know Embroidery Library has some good tutorials on card making. That might help as well as their designs. They do list designs that are appropriate at the end of their tutorials, but I do not know if cupcakes are included. But I do know one tutorial uses fabric with card making.

Make up (fold) the outer card from stock card in your choice of colour. Cut out a window in the front of the card to the size required to display the embroidery design leaving a border of card of approximately 0.5" all round. Glue the embroidery to the inner face of the front cover, ideally leaving a narrow edge of card not covered by the embroidered material. Cut and fold two pieces of a good quality paper (colour of your choice) to fit the main card dimensions. One side of the fold of the first of these two pieces is then glued to the underface of the embroidered material with the other side left free. The second folded piece of paper is then placed as the central leaf and secured to the main card using a coloured ribbon (or similar) tied in a bow on the outside of the card fold.