Is it permissible for branches of the civil company to take an additional amount from employees when disbursing salaries via smart card, and does the employee incur a religious burden by this? And is it permissible for a sheikh to pray over a non-Muslim deceased if there is a benefit for Muslims in doing so?

The company that provides banking services to workers and facilitates the withdrawal of their salaries is not permitted to take a sum of money from the workers in exchange for these services, unless the workers willingly agree to it. This is because the agreement was made between the company and the bank, not the workers. This has no relation to usury (riba). As for praying over a disbeliever (non-Muslim), it is not permissible according to Islamic law by consensus, due to the Almighty's saying: "And do not ever pray over any of them who has died or stand by his grave. Indeed, they disbelieved in Allah and His Messenger and died while they were defiantly disobedient." And whoever is coerced into praying over them, the sin is upon the one who coerced them.