For example reading content in files uses more resource than just examining file names and dates.
Another important thing: FJ will scan everything when a rule starts first time, because it cannot know what has happened when the rule wasn't running. This means there is an initial load of work when File Juggler starts and when you create or change a rule. Once the rule has examined everything, it will be notified of changes in your folders, and cpu/disk usage will drop
When File Juggler examines your folders, it runs in low priority, meaning that windows will prioritize other applications higher. So in practice you shouldn’t really feel File Juggler working, when you use the computer.
From version 1.3.14 the log writes when a rule is examining its folders, so it's easier to see what File Juggler is doing.