Which Version of SEP you are using ? Which Scan you want to perform ?
If you have11.xx U will have performance issue. If u have 12.1.xx u will not see any performance issue.
As sep 12.1.xx does not scan files again & again unless untill it had modified.
SEP Tags it as scanned and does not scans again.
After Migrating to SEP 12.1 We are doing Daily Active scan & weekly Full scan in our company.