Yeah... I seem to recall beer not being a problem. I'm not sure I'd want to rely on beer to keep me hydrated, though, since the alcohol is a diuretic
One thing that struck me as unusual was that when I was at the convenience store trying to scare up some bread for the wife, I noticed that the bread shelf wasn't entirely empty. There was pretty much a whole box of this one particular kind of stawberry-looking snack cake -- and nothing else. I probably should have made note of the brand or taken a picture. You can't possibly find a better dis-recommendation for your product than having it be the last item left on the shelf after a disaster and still nobody will touch it.
Also, it helps to think outside the box. A day after I struck out on bread, a friend of mine told me she had been buying bread from a small corner bakery a few blocks further down the street and when I checked it out, sure enough... the guy was just pulling several loaves of fresh bread from the oven. Of course, I know I can't rely on that bakery in the event of a huge local disaster but the point is that you also don't have to rely on just-in-time distribution to the chain stores -- pretty much every neighborhood in Tokyo has mom-and-pop shops that supply basic staples and it might be worth getting to know where they are and what they sell (and maybe doing a bit of business there from time-to-time) before the next big one hits.