We won't really know what is going on until some sales reports come in, or the next earnings report. Maybe they actually made a ton of Shuffles and Mac Minis and are still sold out (that would be great!), maybe they had supply chain issues and were not able to make as many as they wanted (bad), maybe they underforecasted (also bad), or maybe its a combination of all of these factors.
In a perfect world there would be just enough available, but if the problem is that the sales have exceeded Apple's already high expectations, then that's a good problem.
Opening another store has no impact on manufacturing more hardware, they're totally separate divisions at Apple. Of course as a whole, Apple has a certain operating budget, but in the case of the Mini and Shuffle I think it has more to do with the general difficulties of ramping up manufacturing than anything else. It's easy to say "Build more factories!", but it's another to try to successfully forecast and do these things, 18-24 months in advance of the lauches.