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