Is the problem too many rules or too many folders or both?
To deal with too many rules, you should look into consolidating them. If there's a common pattern to them, you should look at match patterns (search the in-app help).
If too many folders and a bunch of them (a) are under a common folder and (b) have the same or similar rules, then instead, you should have Hazel watch the common folder and then have it go into subfolders to apply the rules. See the sticky article near the top on how to do that.