I guess we have been lucky, we have over 1000 iPads delivered and handed out without a single empty case in 2012. I have returned two iPads to Apple because the screen was unresponsive and Apple replaced them within 3 or 4 business days.
We have not started adopting iPad mini's yet, but I'll keep an eye for theft such as yours.
Sorry for your shock, frustrations, loss and reimbursement. I love credit card companies.... well maybe just really like them.