The following article contains spoilers from Dark Crisis: Young Justice #2, on sale now from DC Comics.
The mystery of who kidnapped Young Justice is still unknown, but Dark Crisis: Young Justice #2 (by Meghan Fitzmartin, Laura Braga, Luis Guerrero, and Pat Brosseau) may have given fans their first clue. In the real world, Wonder Girl sought out the help of Arrowette to investigate the boys' disappearance. Her flippant attitude, visible anger about her past, and blatant attempts to not put in any effort seem to imply feelings of guilt.
There are a few holes in this theory, but thus far no viable candidate has been given for who could have taken the boys -- or even why. Arrowette, however, has a shocking amount of bitterness towards Young Justice, the boys especially. Her actions since their disappearance seem to suggest that she had, at least, a little something to do with it.
The first implication of this theory -- motive. Arrowette has expressed her disdain for her past with the team. She rightfully points out that Young Justice is not only a toxic environment for the teens, but also fights people who are simply trying to do their best in life. Arrowette also reveals a specific dislike for the boys, calling them "three privileged idiots" and went on to elaborate on how their disappearance isn't a problem for her. It seems entirely plausible that she may even be happy that they're gone. In her eyes, the world revolves around them, and she is nothing more than a side character, something she resents and is more than happy to leave behind.
Arrowette's recognition of how difficult the past was for her might be all the reason she needs to try and remove Young Justice from her world. Perhaps she genuinely felt the world was better off without them in it. Which in turn, results in her getting rid of them instead of forcing the world to continue to endure their privilege.
Her words are supported by Young Justice's fight with the Mighty Endowed, then Tora, and later on the behavior of their mentors. These events seem like more than just mere coincidences. It's almost as if the world is responding to what Arrowette is saying and making it a reality.
Perhaps the biggest hint of guilt came when she and Wonder Girl approached Red Tornado. While Wonder Girl asked for help, Arrowette rejected her and even tried to dissuade her. Not wanting to help is one thing, but trying to stop others from helping hints at something more sinister.
However, there is a flaw in this theory, Arrowette doesn't have any superpowers. She's an archer, an excellent one, but not a supernatural being capable of altering reality. Thus far that power only belongs to Pariah. But, Arrowette also spent some time out of the spotlight, so there is no confirmation of what she did or what happened to her during that time. She may have acquired powers behind the scenes and kept it a secret.