Yes! AlphaFold does appear (at least to this non-expert) to actually advance Chemistry. But I have seen nothing that I would call evidence that Hinton’s work on the “Boltzmann machine” has contributed anything to understanding of the physical models that inspired it. I expect that this will be a controversial award!
Source: (15) Two Nobel Prizes for AI, and Two Paths Forward
See also this video and this from a couple of other surprised physicists.