What is the ruling on disposing of money unknown to the heirs, which was secretly given to one of the sons before the father's death by his niece who owed the deceased, and is it permissible to donate it to mosques without informing the rest of the heirs?

The money repaid by your grandfather's granddaughter is part of his estate and must be delivered to the heirs. The debtor must inform the heirs, but if she fears mischief, then you should ascertain each heir's share and deliver it to them without their knowledge. It is not permissible to give the money in charity because it belongs to specific individuals, in accordance with Allah's saying: (Indeed, Allah commands you to render trusts to whom they are due) and the Hadith: (On the hand is what it took until it renders it).