Is it permissible for me to take the annual profits that the company grants to employees, knowing that they are a mix of what is lawful and the company's profits from taxes on goods and berths, and sometimes from assisting ships in importing and exporting alcohol?

There is no harm in benefiting from the profits given to an employee by the company, as long as his field of work is permissible, even if some of the company's resources are unlawful, due to the permissibility of dealing with someone whose wealth is mixed [with lawful and unlawful sources].