If I see a file with no code I'll look for the docstring and the header comment to see what's the deal, why is that info there. If I see an empty file I've nothing to look at. I haven't tested but sphinx may generate documentation for that empty file for having a docstring.
Anyway, is more a preference than a 'should do that way', if you feel strongly that all the files including the empty init ones should have the header, I'm ok with that.