Hi,
I am not 100% sure if GpgSM (the S/MIME part of GnuPG can’t handle them. I am sure though that Kleopatra does not support it in the Smartcard Management view.
You could try it out by inserting the card and on the command line use:
gpgsm --learn-card
the OpenPGP part of GnuPG (gpg) will not be able to handle it.
In general S/MIME certificates like you have and OpenPGP are incompatible. While in theory the underlying key material could be reused in practice it does not make much sense and is not supported by GnuPG directly. Yes it would make sense in the case of smartcards but the S/MIME and OpenPGP card specs differ.
If you switch from S/MIME to OpenPGP you will have to publish / provide new public keys anyway.
So my suggestion would be to get an OpenPGP card, do OpenPGP with GnuPG and that card and maybe keep your old S/MIME card around and do S/MIME with that.
Best Regards,
Andre