I am running squidguard on a SME 6.01 server.  supdate.cron is located in /etc/cron.daily.  If you look at /etc/crontab, you will see that cron.daily gets executed at 4:02 am.  So, you could change the time that cron.daily gets executed, or create a crontab entry for supdate.cron to run at a time that is good for you.
GL,
JB