What is the ruling on money earned from working in a company that uses unlicensed software (such as Windows), knowing that the company intends to purchase licenses gradually, and that the absence of licenses may expose the company to closure and fines?

If the company uses a system belonging to other parties without their permission, this is an infringement on the rights of others and is not permissible. Accordingly, if you use this system in your work, your work is not permissible. However, if you do not use it, there is no harm in your work.