The setting controls how far a Complete Scan will drill down into the directory tree. The default setting is -1 which means infinite depth or all sub-directories (recursive). The only reason to change this setting would be if you had a recursive symlink in your path or a directory problem that prevented the Complete Scan from finishing. Then you could experiment using different low integers until you found the level that worked for your given situation.
Example:
If you scanned the wp-content directory with a Scan Depth setting of 1 it would not scan any of the sub-directories. If you used a Scan Depth setting of 2 it would scan:
…/wp-content
…/wp-content/plugins
…/wp-content/themes
…/wp-content/upgrade
…/wp-content/uploads
and any other directories directly inside wp-content but none of the sub-directories inside those first level sub-directories.
Note: By using a positive integer as your Scan Depth setting you will likely be skipping branches of your directory tree that might contain the malicious code you are looking for, so it’s best to use the default setting whenever possible.
Please let me know if you have any more question.
Aloha, Eli