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 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 enough to say Tasbeeh (Saying Subhaana Rabbiya Al-‘Atheem during Rukoo`, and saying Subhaana Rabbiya Al-A‘laa during Sujood ) once, or twice during Rukoo`(Bowing in prayer) and Sujood (Prostration)?
All perfect praise be to Allah, The Lord of The Worlds Yes, saying Tasbeeh once during Rukoo` and Sujood is enough, provided that the worshiper`s attentiveness of the heart isn`t undermined during each. As regards the recompense, it depends on the number of Tasbeeh. And Allah Knows Best.
Is it permissible to offer prayer at home, or should it be offered in the mosque?
All perfect praise be to Allah, The Lord of The Worlds. It isn`t preferable for the man to pray at home as praying in the mosque is twenty seven times more rewarding. Therefore, this should motivate him to offer prayers in the mosque. And Allah Knows Best.