If you use the CLI version of FanFicFare, you could script a crontab
job. Calibre has an auto-add from directory capability, but you would
lose FFF's ability to set various columns.
There isn't any sort of cron capability built into Calibre.
The 'Proceed to update Library' dialog is something the Calibre dev
strongly recommends. Some plugins disregard that, but FFF follows it
for safety.