Using and applying security tools and scanners is all about applying a correct mindset. In general, people that use 'hacker' or security tools with good intentions such as authorized auditing are called 'white-hat' hackers. Conclusion Security scanners are valuable tools in improving your site's security, but they should be used with common sense. It is not because your scanner doesn't detect the hole that there isn't a potential future one. New holes are being found every day and your scanner will be rendered useless if you don't update it often enough or fail to act on what it reports.
Complete security is a goal that can never be attained.
You can only strive for it. But checking the pulse of your systems is a good start.