Is the salary considered permissible or impermissible if the company owner possesses wealth with religious doubt, even though the nature of the work itself is permissible?

There is no harm in working for a company whose activity is permissible, and it does not matter if the owner's money contains a trace of unlawful earnings, because the unlawfulness is not attached to the money itself but to the owner's responsibility. The default assumption for a Muslim's wealth is that it is pure and permissible, and there is no need to investigate its source.