I have installed search configuration module to alter pagination on search results. I've set the pager limit in Configuration > Search settings > ADDITIONAL NODE SEARCH CONFIGURATION > RESULTS to 3 (which should trigger pagination), but no pagination is appearing when I am logged in whereas when I am logout, it is showing pagination having 2 items per page instead of 3.
This is, presumably, by design. If you look at Search Config's query alter function, you can see that the function returns (without limiting results) if you're you're the superuser. Hence, when you're logged in with UID = 1 you will not see the pagination.