Here's what DNA Doe Project said on facebook when I asked them if they still weren't taking on child cases:
'you're correct. Due to the age of the Boy in the Box it is unlikely we'd be able to take his case. Too likely that family was involved since no one reported him as missing. There could certainly be scenarios where the family is innocent, but we can't take that chance. It's possible that Colleen could analyze the Y-DNA, but that would not be through DNA Doe Project.'
And they are going to see the Boy in the Box's agency at Rootstech this week, which I guess is a conference about these things