The phrase was coined by HCL Finance as a name for one of their finance products. They were especially prominent during the United States housing bubble of the 2000s but have gained wider notoriety due to the subprime mortgage crisis in July/August 2007 as a prime example of poor lending practices2. The term grew in usage during the 2008 financial crisis as the sub prime mortgage crisis was blamed on such loans. It works on two levels - as an acronym; and allusion to the fact that ninja loans are often defaulted on, with the borrower disappearing like a ninja.
Business dude 2: "Haha, I expected that; he sure pulled off a nice ninja loan!"