I think between the iPhone 5, iPad 3, iPod touch, iPad mini ans iMac refresh, they simpy don't have the production resources to also focus on the Mac mini line.
I've considered that too but since Apple essentially outsources all production this doesn't seem to hold much weight in my mind for more than a few seconds. There are plenty of companies that have production capacity available for fulfilment. Maybe internal(to Apple) engineering resources might be a more valid shortage? Cash reserves point to something else all together though...not heartening.