Is it permissible to work for a company that tells foreigners its employees are not Egyptian, when in fact they are, under the pretext that this prevents dealing with them, and does the responsibility for this lie with the company owner or with the employees?

If your work is permissible, and you perform it as required, and you do not participate in lying or forgery, then there is no blame upon you for working at the company and benefiting from the salary. As for the company owners' lying about the nationalities of their workers, that is a reprehensible act that you must denounce with your hand; if you cannot, then with your tongue; if you cannot, then with your heart, and that is the weakest of faith. Explain to the officials the impermissibility of their action. If they do not desist, and you are able to clarify the truth to the clients, then do so. Otherwise, denounce it with your heart.