Will my salary be affected by the fact that the company owner deals in usurious transactions, and what should I do to ensure my money is 100% halal?

As long as your work in the company is permissible and you perform it as required, the salary you receive in return is permissible. It is not affected by what you mentioned about the company owner sometimes dealing in forbidden ways. As for your feeling of a lack of blessing in money, that is part of the unseen, and there may be other reasons for it. Among the causes of blessing are moderation in spending, charity, maintaining kinship ties, and supplication.