A crime of this nature, theft from a business, by someone in the business, is a very serious matter; and takes a lot of work to defend. The evidence is usually a few boxes full of paper, and it takes going through it all to be effective.
In theft from business cases, oftentimes an employee will admit to taking the money, but there will be a dispute as to how much money is stolen. My experience with these cases is that money is easily stolen because the business is being run poorly from a financial perspective. It takes far too long for the theft to be discovered. Which brings up issue related to prescription, and more importantly, the amount of money missing. If it takes a business a few years to discover money is missing the record-keeping is suspect, to say the least, and that poor record-keeping casts serious doubt on the amount of money stolen. Keeping in mind that most people will make insurance claims on the stolen money, and generally inflate the figures.
I am not saying this is the case each time, just that a skilled defense is necessary to make sure the defendant does not get stuck with a crazy restitution.