Is the 5% increase on the delayed salary, which the company approved one time due to the delay in disbursing salaries, considered usury?

There is no harm in taking an unconditioned increase on a delayed salary, because a deferred salary is considered a debt. If the debtor repays more than what is owed without a prior condition, then it is permissible. This is supported by the Prophet's ﷺ saying, "The best among you are those who are best in paying off debts," and Ibn Qudamah's statement that if an absolute loan is repaid with something better by mutual consent, it is permissible, unlike a conditioned increase, which is considered a loan that draws benefit. Ibn 'Uthaymeen clarified that an increase in banking transactions is customarily considered conditioned, unlike an unconditioned increase in repaying a debt.