Nikto is not designed as an overly stealthy tool. It will test a web server in the quickest time possible, and is fairly obvious in log files. However, there is support for LibWhisker's anti-IDS methods in case you want to give it a try (or test your IDS system).
Not every check is a security problem, though most are. There are some items that are "info only" type checks that look for things that may not have a security flaw, but the webmaster or security engineer may not know are present on the server. These items are usually marked appropriately in the information printed. There are also some checks for unknown items which have been seen scanned for in log files.
Nikto is written by Chris Sullo and David Lodge.