I believe it counts all actual physical disks on systems that are being monitored, regardless of how they are set up.
Some details on what to check to compare the license disk count with the arrays:
The table used to get the total disk count for licensing is, ent_san_storage_current
You can check that or the Executive Storage Summary report.
You can also run a Physical Disk report from quick reports under each array category, see what the total count is.