Actually, looking at the code changes between 1.0 and later versions, I don't see any changes in that regard. AFAICS, the plugin has always worked on all products (published and unpublished), so version 1.0 wouldn't help you. I have put your suggestion on my TODO list, but I can't promise anything yet.
Best regards,
Reinhold
PS: In version 1.0 there was a bug that only the first 15 categories (or whatever pagination setting you have set for VM) were used. Maybe by unpublishing a category, that category fell out of the categories used and thus you observed that result. But that was due to the category ordering and not the unpublishing itself. It rather meant that also some other categories were accidentally excluded.