just edit the times in your cron job files, the second collumn is the hour of day field so thats the one you want to edit eg to set the above jobs to before 1am you would edit them to look like:
25 0 * * * daily
47 0 * * 7 weekly
52 0 1 * * monthy
they will then run between 12 and 1 am instead of 6am
its likely that when your server installed it randomly generated the time (so that it prevents every server in the world checking for an update at exactly the same time which would probably cause a whole lot of problems if they did) there is no particular reason to run them at that time, but it does make most sense to run them outside the general working hours that the server is in most use for.