An English techie named Dean Murphy developed Crystal, but the technology that lets certain ads evade the blocker comes from a company called Eyeo GmbH, which developed the popular desktop application Adblock Plus.
Adblock Plus is free, and its developer is currently accepting payments from approximately 70 companies that want their ads to show up even if people use the app to block them. According to The Journal, those companies pay Eyeo, and Eyeo in turn pays Murphy to include its so-called "white list" in Crystal. Ads from companies on that white list will appear on iPhone and iPad screens, even when Crystal is turned on. Eyeo also plans to make similar deals with other developers. The company says ads that evade Adblock Plus must comply with its "acceptable ads" policy, which stipulates that ads can't be too disruptive or intrusive.
Crystal is far from the only ad blocker on Apple's App Store. Some options are free, some are paid, and many of them are very popular. In fact, an ad blocker app called Peace rocketed to best-seller status as soon as Apple enabled ad blockers in its new iOS 9 software. Marco Arment, the creator of Peace quickly pulled the app, however, saying in a blog post that he "just doesn't feel good" about the current situation. (Android users can also download ad blockers.)
Arment raised an interesting point. On the one hand, ads, particularly those users view on relatively small smartphone screens, can be very annoying. They often slow things down, take up all of the screen space or launch self-playing videos. On the other hand, someone has to pay for content online, and like it or not, that generally means ads, though more and more publishers put their content behind paywalls.
The tension between users and advertisers sparked something of an arms race. A number of companies created apps that defeat ad blockers, and Hulu, for example, will not let visitors view its content if they use ad blockers. Hulu offers an ad-free version of its service, but it costs extra $12 a month.
I honestly don't know how to resolve the issue. I do, however, feel strongly that transparency is a necessity. If an app only blocks some ads, it should be clear about why. And if a site uses software to block the ad blockers, it should disclose that too, similar to how some sites now inform users that they use cookies for tracking.