Default excluded directories are documented here: Excluding directories from being scanned
In the BigFix Console, the Action history of Tasks 63 & 64 (Systems Lifecycle Domain, IBM BigFix Inventory Site) will tell you who may have modified the Excluded Directories settings, and when, if it was accomplished by a BigFix operator.
Excluded directories may also be adjusted manually:
You specify those directories by adding paths to the exclude_path.txt file that is in the <BES Client>LMT/CIT directory. Each path must be added on a separate line.
So there is a possibility that someone with sufficient administrative access could have modified this file directly.