Is an employee sinful for helping his employer sell state-subsidized food items on the black market, knowing that the majority of companies do this?

You bear the sin of aiding in the commission of a forbidden act. It is not permissible for a merchant to sell subsidized goods on the black market, as this involves unlawfully consuming public funds, violating contracts, and oppressing consumers. It is obligatory to advise him, and if he does not accept, report the matter to the authorities to stop him.