Snap judgments are often incorrect. The Daily News is not terribly likely to have ponied up a lot of loot to a photographer for fakes. In context with all the other shots included in the sequence, there is no reason to suppose the frontals and ass crack are ringers, like the kind of edited crap inserted into dishonest Planned Parenthood smears.
When you check out the entire sequence at The New York Daily News or other site, you might also discover larger and more clear images that do show the "missing" ink. There has been some discussion of what can be seen via telephoto lens operating from a considerable distance, but at least the Canadian has not himself denied anything, which if they were, in fact, fakes, he should have done by now. It's not as if acknowledging the alleged fraud would help promote it.
Also, as it happens, and for whatever it is worth, Justin's father Jeremy does not seem to have any doubts. In typically classy faction, he has tweeted admiration for his son's apparatus:
The tweet: "@justinbieber what do you feed that thing. #proud daddy"
That may not be dispositive, but it works for me. Arianna's Clickbait Gazette revealed the parental acknowledgement:
http://www.huffingtonpost.com/entry/justin-bieber-jeremy-bieber-tweet-penis_5617fc82e4b0082030a26722