Is a person considered a thief if accused of taking the livelihood of their former employee who was late and absent from work, and then the employee claims that they were hiding sales from them?

The contract is not precisely clear, but if its implication is that the worker receives a percentage of the profit from each item he sells, then it is a contract of ju'l (a stipulated reward for a specific task). In such a contract, the worker is not entitled to his wage unless he performs the stipulated work according to the required description. So, if you did not wrong the worker and did not withhold any right he was entitled to, then there is no harm upon you; rather, he is the one who wronged you, and he is not entitled to payment for work he did not perform.