Is it permissible to take the deserved payment for overtime hours without the employer's knowledge, after he refused to pay or compensate for them, knowing that he used to pay less than what was agreed upon and less than what engineers are paid, and that he was well-off?

The determining factor for the daily working hours and their duration is the agreement between the worker and the employer. If the contract stipulates 48 working hours per week and you have agreed to it, then you are not entitled to claim compensation for something you have consented to. It is not permissible to take compensation for this from the employer's money without his knowledge, even if you worked extra hours voluntarily. It cannot be definitively asserted that you are entitled to anything from the employer that permits you to take from his money without his knowledge. It is recommended to speak directly with scholars to clarify your right and to return what you have taken if you are not entitled to it.