It doesn't harm the system if you don't have those cron jobs run, but it is certainly recommended because it helps the computer run faster by deleting unneeded cache files, among other things. However, becase Unix was originally for servers that were on and active 24/7, the maintenance script was set to run around two or three AM in the morning, a time that would have been unobtrusive.
These tasks can be run manually either from the Terminal or by using some third-party app such as MacJanitor or Cocktail, eliminating the need for the computer to be on all night. Remember that if the computer is on sleep, these scripts don't run. I run the cron jobs manually and either shut the computer down or let it sleep at night, depending on whether or not I have to use it the following morning before I go to school. I haven't heard anywhere that it is bad to shut the computer down every single time, but just a matter or convenience for most people.