GnuPG should learn OpenPGP keys and S/MIME certificates stored on smart cards automatically when a new card has been seen. Currently, Kleopatra (and other clients) have take care of this.
This is a spin-off of T7379 where @werner wrote:
The whole learn-card thing is more a hack than a solid way to make cards known. We should do such things in the background when a new card has been seen.