The Plugin Guard scan will look inside your plugin folders and determine if anything is changed, added, or missing.
If you have 10 plugins installed, that's 10 folders to look inside.
That is if your "scan depth" is one (1). 1 means "1 level".
If you change your depth to two(2), the scanner will look in the first level and the 2nd level - ie. if there are any subfolders inside a plugin folder, it'll look in there too.
If your depth is three(3), the scanner will look inside the sub-folders of the sub-folders. And so on and so forth.
As you can imagine, the deeper the scan, the longer it takes and the more resources it uses.
By default, the scan depth is 1. You can increase this as much as you like, but you must understand that the more levels, the more time/resources to scan each time.
To scan all levels of a plugin/theme folder, set the scan depth to zero(0). When it's at zero... every sub-folder inside a plugin/theme will be scanned.