It's crazy auditors didn't spot discrepancies especially with the high base rate of reported frauds and errors, but if finding the receipts for stolen money was the threshold for prosecution any remotely competent thief would be in the clear
If there is absolutely nothing to corroborate the money going missing, no evidence presented for where or how the money was stolen then there shouldn't be enough to send someone to prison.
The amounts of money involved may be small to business owners in other domains but for SPMs many were almost bankrupted by trying to replace the sums out of their own earnings as you say. This wouldn't have been a rounding error to their lifestyle, it should have been provable to any halfway decent investigator. And if not? Then they get away with it and it's the price we pay not to live in tyranny.