SEP and VSS

I was wondering if SEP 12.1.6 scans Microsoft Shadow Copies.  Ocer the past few weeks I've noticed my nightly scans taking longer, sometimes even running over a 36 hour period or not ending.  The drive I'm scanning onlyhas around 200,000 files located on it, but the log of a scan can be close to 4,000,000 files.  I've gone into the scan and excluded system volume and $Recycle.bin from the scan.  Would it be a better idea so split my scans up?