These are available in other places. For instance, you can "Hide user list and data from guests" in ACP -> Settings -> User
Disable Reputation System option seems incompletely implemented.
This is probably old news, but there seem to be some parts of the reputation system that never really disable. Specifically, it says: "Reputation: * 0" at the bottom of every post and there is still a button to list users by reputation (/users/sort-reputation).
It seems like checking the "Disable Reputation System" checkbox should remove both.
Disabling reputation system only disables privileges tied to reputation like managing threads or content after you gain X reputation, it wasn't meant to disable the whole reputation system. Maybe it needs better wording in the ACP.