Is it permissible for the husband to take an amount of 2400 Riyals from the pharmacy's income without the employer's knowledge, in exchange for the work permit fees that were deducted from his salary, believing that he is entitled to it and that the employer wronged him by deducting it?

The reference for determining who is obligated to pay the fees is the party that imposed them:

If the fees are on the employee, your husband is obligated to pay them, and he must return what he took from the employer's money without his knowledge.

If the fees are on the employer, your husband is permitted to take what compensates him for what was unjustly deducted from him, if he cannot recover his right by other means.