Is there any recommended procedure that should be followed for rebooting the SCOM environment on a timely basis for maintaining the health of the server, also when new stuff(monitors, rules, network devices) is added in SCOM does it have impact on system files that would require a reboot? 

Updates of monitors, rules, MPs, etc. don't require a reboot. The only time our management servers get rebooted is when they're getting patched. Sometimes, I'll clear cache manually on a server if it seems like SCOM is off in the weeds. (Stop MMA service, delete Health Service State directory, restart MMA)