Not sure how a smartcard is related to "autorun a logon script"?
Anyway. Floppy disks cannot act as full-featured smartcards. (They don't even have any electronics in them, which a smartcard would need to perform cryptographic ops.) So that could be done if you gutted the disk and the drive, and glued an actual smartcard in one, a card reader in the other.
At best, you could use a floppy disk as a sort of simple password-replacement, similar to how https://github.com/aluzzardi/pam_usb works for USB sticks – it would probably work with /dev/fd0 with only minimal adaptation.
The PAM module works by checking that the disk contains a secret file matching some hash, and even has some basic protection against copies/replays by regenerating the secret on every login (since the floppy disk itself is just a 'dumb' storage device & cannot prevent someone from simply copying the "secret" file).