ideally it should not cause any issues.
you can consider create exclusions for your necessary programs. and known issues for client failure
Troubleshooting client installation failures
http://www.symantec.com/business/support/index?page=content&id=TECH94258
creating exceptions
Troubleshooting client installation failures
http://www.symantec.com/business/support/index?page=content&id=TECH183201
for windows servers
Best Practices for Installing Symantec Endpoint Protection (SEP) on Windows Servers
http://www.symantec.com/business/support/index?page=content&id=TECH92440