Is the salary received for vacation days, which the employer counts as working hours to avoid deductions, Islamically permissible, given the danger of being at work on those days and that this system has been ongoing for four years?

If your manager's cooperation is authorized by the workplace, then there is no blame on either of you. However, if it is not, then what you both did is impermissible, because it is consuming people's wealth unlawfully, through deception and falsehood, and this is forbidden by Sharia. If working alone poses a danger to you, then you should take unpaid leave. If what you took was unlawful, it must be returned to the company by any suitable means that does not cause embarrassment.