I don't really see the point of generating hashes and comparing them, it's very time intensive, that would slow the export process down. If it's the same file (same path and name), it won't be packed two times, but if you have two equal files there is nothing done about that. That's something the game developer must handle by not duplicating the files.
Hmm interesting. What I was thinking of though was just hash the files at the finalization/packing step so that the files are only stored once. I don't know how other developers workflows are, but if other tools are used to break apart animation frames to use in the game engine, there may inevitably be the same images or audio reused a dozen times with different filenames.
Anyway it was just a suggestion I thought I would mention. I'm still evaluating if Visionaire is the right tool for a project. iOS target being one of the consideration points.