That's only if Pokemon breed through sexual means; they may not even have sex organs, since they are not depicted with any. There is a theory held by myself and others which states that when Pokemon breed, it is simply a matter of pooling the two Pokemon's energies together in order to materialize an egg.
Anyway, in response to the OP, I've always believed that those "clothes" are actually just their (very abnormal) skin.






















ALL HAIL LORD GHETSIS!!!!!!!!!!!!!





