My communities are visible to the Moderators and Stack Exchange employees, Its fine. But it says, "Other people may also be able to associate your presence on those communities with your public list in certain cases." If other people also can see my hiding communities then what is the uses of Hide communities here in Stack Exchange? Every general users are able to see my communities here.
If other people also can see my hiding communities then what is the uses of Hide communities here in stack?
Well, your communities are hidden from other users in your profile. That doesn't mean your activity is invisible. If you interact on the site, you will just appear to be there as others are, your account doesn't get 'linked' to your other profiles on other sites.
That means that this feature is only really useful to unclutter the list and emphasize the sites you care about, not those you are registered to to flag spam.