Is it permissible to take the salary deposited in the account along with the King's مكرمة (royal grant/honorarium), knowing that the contract had ended and all dues were received before this amount was deposited?

It is not permissible for you to take the money that was mistakenly deposited into your account without referring to the responsible authority. If they permit you to benefit from it, then there is no harm. Otherwise, it is obligatory to return it to them. Neither generosity nor the fact that it comes from the public treasury makes it permissible to take it without fulfilling the conditions for its entitlement. Therefore, the source of the money must be verified through the responsible authority.