I was thinking about "How much data could be squeezed into the $2$D QR code", then it stroke me, that if it were a $3$D cube, probably inner voxels would be hidden from the outside observer/scanner. So there will be little usefulness of such codes.
The questions, that I find hard to answer are:
If I was an $n$-dimensional creature, would I be able to scan a $n-1$-dimensional "QR"-code without any problem, as we do with $2$D version?
or rather,
would I still be struggling to read even $3$ dimensional version?

I think you would be able to do so. For a 2D creature, seeing the inside of a square from outside is impossible, for us it's trivial since we can look at it from "above" (by moving to a plane parallel to the square). Similarly, a $n$-dimensional creature could move along the $n$-th axis to a $(n-1)$-dimensional plane parallel to the $(n-1)$-dimensional qr code. Maybe this non-formal answer could be better suited for a comment but I can't leave them yet.