In Safari, autofill and passwords are saved by default and in a separate silo from the cookies and cache. In Safari > Preferences, you will probably see tabs for Autofill, Passwords, and Privacy. Under Privacy is where you can click Manage Website Data to remove web caches. Clearing your cookies and cache will result in you being logged out from your websites, but it will not remove previous autofill or saved username/password information.
You only really need to clear your cache and cookies if you are experiencing browsing issues or have privacy concerns.
I hope that helps answer your question!