I really doubt that Batman knows, for the following reasons:
1. It seems to be legitimately the case that Batman leaves it to the Team to handle their own problems. Considering that Nightwing is now in control, I imagine that has only been even more the case. Batman has no motivation or interest in paying attention to the team with everything else going on.
2. Batman is the obsessive type. A long time passed where they had no idea what happened during the 16 hours, and I'm sure Batman didn't just drop that. It was probably driving him mad trying to find leads down that road. With that and all the other signs and tech, he may well have suspected alien involvement, but didn't have a break in the case. Any way you look at it, though, he was probably much more focused elsewhere.
3. Nightwing is just like Batman. It's a reality he struggles to face in most continuities, but it really is true. And what comes along with that? Deception and misdirection. Essentially, Nightwing and Aqualad's big plan is a giant batman gambit on multiple levels. Nightwing is enough like Batman to be able to keep his distance and keep people off his trail. I'm sure that he has gone out of his way to keep Batman out of the loop.
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