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.
What is the ruling on one who performs ablution or the ritual bath while having nail polish?
Nail polish must be removed before ablution or ritual bath so that water reaches what is beneath it, because it is a barrier that prevents water from reaching that area. This is based on the hadith narrated by Ali (may Allah be pleased with him) from the Prophet (peace be upon him): "Whoever leaves a hair's breadth of his body unwashed from major impurity, such and such will be done to him in the Fire." (Reported by al-Bukhari). And Allah the Almighty knows best.
How many Rak`ahs (unit of prayer) are offered in Witr prayer?
All perfect praise be to Allah, The Lord of The Worlds Witr (an odd number prayer performed between Isha`a and Fajr) is offered with a minimum of one Rak`ah, and a maximum of eleven, but offering three Rak`ahs is the minimum of its complete form. And Allah Knows Best.
What should a person, who doubts the validity of his Wudu, or over performs it, do?
One who doubts the validity of his/her Wudu while performing it should redo it until he/she is certain of having attained purity. But, if doubt was after having performed Wudu, then he/she should not pay attention to that as doubt after the end of an act of worship does not count. This is of course in case doubt was within the reasonable limits since once it goes beyond that, it becomes a whispering of the Shaytaan (devil) which he/she should ignore as the Wudu is valid.