I have the Answer! c(: It clicked on who has it when I reread the series.
Apocryphos (also known as Cardinal) Says in Chapter 213 page 7 "I understand Please Leave it to me. My lord. He who carries the "heart". Yes. I will defend you for certain." during the scene of when Allen is saved by the Noah and Link declared dead. That crosses Lenalee out of having the heart of innocence because Cardinal says he, and that also crosses out Kanda for he wasn't there at the present time and was without his innocence. It only leaves Allen. Since it is also certain that Lavi doesn't have it either because he is a bookman and is supposed to report to Bookman if enything weird is starting to happen.
So the Answer is Yes Allen has the heart of innocence.Even before chapter 213 there has been clues leading toward Allen having it.
Allen lost his arm but his innocence didn't die.
Allen was also saved by his innocence.
Allen's revived innocence can turn into the opposite colored sword of the Earl.
And also note that Allen's innocence seems to be in two pieces. The mask and the arm/sword.
Lenalee's innocence protected her with a crystal but you can also say because the innocence was ready to evolve into a crystal type innocence.
Kanda's innocence also became a crystal type innocence.
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Allen and Lenalee are the true wielders of the Heart.
Their Innocence are the most powerful.
ralph wept for the end of innocence, the darkness of man's heart...
To activate his innocence and to get his arm back he has to know what he truly wants to do in his heart and finally decides that he will save humans with his right hand and akuma with his left. This reactivates his innocence turning him into God's Clown, also known as Crown Clown
"Ralph wept for the end of innocence, the darkness of man's heart, and the fall through the air of the true, wise friend called Piggy." The Last line has two significant meanings: 1. Ralph cries at the end, because he realizes that he will never be the same again. His innocence and childhood were now all gone. 2. Ralph learns how evil and dark man can be. He realizes how in every man, there is always darkness in their heart.
Only once at the end of the book when he releases all of his emotions out because of the "loss of innocence, the darkness of man's heart" and the death of Piggy.
D Gray-Man is for ages 13 and older, only because of the violence and swearing, but that's it