Mongdb start up warning logging
Startup warnings shown in the mongo shell are excerpts from your MongoDB server logs. These warnings do not change until the process is restarted, so if you can't find corresponding entries in your default MongoDB log file I expect that the log file has been rotated since the process was started.
Depending on your environment configuration, old log files are typically renamed and compressed so you may need to search for different file names or use a utility like zgrep to search compressed files.
You can redisplay the warnings via show log startupWarnings or the getLog administrative command.