For example, say John has a drug addiction, but he failed to disclose this on his application. He is eventually granted the clearance, but now he has to keep this secret for the rest of his life. Someone could easily blackmail him for secret government information. If he is caught lying, his clearance will be revoked and he will lose his job, and more than likely he will never be hired for a position that requires a clearance ever again (many US gov't jobs require a clearance).
Honesty is a sign of your loyalty to the U.S. Depending on the type of clearance, you are sometimes required to take multiple polygraph tests, and you will more than likely be caught lying.
Author did the right thing by being truthful.
See http://www.rjhresearch.com/ADR/index.htm for more information.