What happens to your fire cider when...

I don't see any reason why it wouldn't be okay to use. Shaking it would just make it more evenly distribute the various spices and flavorings, in a shorter amount of time. The contents themselves should prevent anything dangerous or worrisome setting up shop in the liquid. So long as you followed the recipe otherwise, and used a vinegar that contained a "mother", it should be some pretty potent stuff by now. I make vinegar myself all the time, and it routinely sits in a dark spot for months without me disturbing it at all. I have no reason to think your mixture would suffer from the same treatment.