Debian 13 "trixie" issues with Nitrokey 3 A Mini

I can confirm that it works great.

One addition:
If you would like to enable the configs directly without an reboot:

gpg-connect-agent "SCD KILLSCD" /bye

also was needed.

If you use xfce also, it can run into problems with pam login issues.
Use xfce4-screenlocker instead default lightlocker:

  apt install xfce4-screenlocker
  apt purge light-locker

and reboot now.

In conclusion:

# scdaemon.conf
    cat <<EOF > ~/.gnupg/scdaemon.conf
    disable-ccid
    pcsc-shared
    loglevel basic
    log-file ~/.gnupg/scdaemon.log
    EOF
# restart gpg
    gpg-connect-agent "SCD KILLSCD" /bye
# using xfce4 => need also:
    apt install xfce4-screenlocker
    apt purge light-locker