Is taking money from their brother’s shop by his two sisters considered theft if they take it without his knowledge, and are they obligated to inform him of that, or is it permissible to return it discreetly without his knowledge as a form of aid?

Neither your brother nor your father are obligated to spend on your studies or your needs. What you took from your brother's money is considered theft, even if the money belonged to both your father and him. Theft is one of the major sins that necessitate the cutting off of the hand and indicates a deficiency in faith. You must repent and regret the theft, and return the money when it becomes easy for you to do so. It is not a condition to inform your brother about this for your repentance to be valid.