Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.
Is bleeding that lasts for nine or ten days considered menstruation (Hayd)?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
If the duration of the bleeding does not exceed fifteen days, then all of it is considered menstruation (Hayd), even if the regular cycle ('Adah) has changed. And Allah the Exalted knows best.
Is supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?
At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.
Is it permissible for the children of a deceased father to settle his debt from the Zakah (obligatory charity) money due on them?
It is impermissible to use the Zakah of one`s money for settling the debts of the deceased. However, children should settle the debts of their deceased parents out of filial piety. And Allah Knows Best.