How to export public keys in PEM format with GnuPG

Use gpg --list-secret-keys --with-colons --fingerprint to generate the list of fingerprints in an easily parsable format. Grab the lines of the form fpr:::::::::xxxx: that correspond to the keys you want to delete, and pass the fingerprints (the xxxx) to gpg --batch --delete-secret-keys.

The following command generates all secret key fingerprints. Be sure to select only the ones you want to delete!

gpg --list-secret-keys --with-colons --fingerprint | sed -n 's/^fpr:::::::::\([[:alnum:]]\+\):/\1/p'

Your export command is correct but as you suppose, the gpgsm's keyring is empty. You can check that with:

gpgsm --list-keys

The output will be nothing.

For your last question: Nope. gpg and gpgsm use different databases. More info is here. You have to create or obtain an OpenSSL key/cert pair and import it (in PKCS#12 format) into gpgsm keyring (usually ~/.gnupg/pubring.kbx) so the import command must be:

gpgsm --import mycert.p12

You can export the keys from one system, convert them and import to another one, but the so-called conversion just supplies the metainfo (in most cases) and a brand new cert/key is being created with that metainfo. You can look here for conversion examples.