Deprecated means the feature will no longer exist in the next major release of Weblogic Server. Although you can still use log4j option for server logging for the 12.1.3 , it is advisable for you to change it to the alternate ones.
Note: You can still use log4j framework for application logging, however the doc you referred is related to server logging. What's New in Oracle WebLogic Server
"The use of Log4j with the WebLogic logging service, as an alternative to Java logging, is deprecated as of WebLogic Server 12.1.3."
The below doc you have read is related to application logging.
Hope this clarifies!!