(It may be appropriate to criminalize failing to pay employees, but I'm not sure about the first and higher-order effects of doing so, or how to craft legal principles and laws with the right incentives, while avoiding special cases like the laundry list of exemptions to California's AB5.)
The difference between “stealing cash” and “wage theft” is only a difference in perspective. The employee didn’t perform any labor to earn the money they took so they’ve broken the contract and now they’re in debt to the restaurant. Likewise, an employee’s labor is a fungible resource they control and the expenditure of it that solely benefits the restaurant through a lie (concealing their actions) is no different than someone scamming the person at the register and walking out without paying.
That's tautological. The actual reason it's a civil matter is because the people who write and interpret the law want it that way, yes?
But, when employers and employees steal from each other, the fact that one is a criminal matter and the other a civil matter says a great deal about the law is and what purpose it was designed to serve.