Considering that it absorbs all chakra based techniques, it's supposed to. Amaterasu is considered a ninjutsu. Though when he used Shinra Tensei to repel the flames instead of absorbing them, it made many question whether or not he could absorb the flames.
My takes on this:
Either Kabuto just had Nagato use Shinra Tensei on Amaterasu for no reason or somehow Amaterasu can't be absorbed.
The only way I could explain it is if I said that Amaterasu isn't made out of chakra or doesn't have anything to do with chakra at all. If this were the case then I don't know how Itachi or Sasuke would even be able to use it since pretty much all ninjutsu are based on chakra.
This would really be confusing so what i'm going to go with right now is that he can absorb it but Kabuto just didn't have him absorb it. If he's not able to absorb it then Kishi should've made a part in which Itachi uses Amaterasu on Nagato again and Nagato attempts to absorb it but then fails. Then some sort of explaination on how Nagato wasn't able to absorb it. I still give Kishi credit for what he did though. The fight was still good though short.
For now, I say yes. That he can absorb it. I just didn't see enough to prove that Amaterasu wouldn't get absorbed. The manga isn't finished yet so hopefully I get to see a better explaination. I doubt i'll see one but well...you never know..
Then again, is Edo Tensei a type of ninjutsu as well? If it is, since it doesn't require the user to waste chakra, perhaps Amaterasu isn't a chakra based technique after all. That is, if Edo Tensei doesn't have anything to do with the users chakra and if it's even a ninjutsu at all.
