Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
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 it obligatory to have the intention for each day of fasting, or is one intention sufficient for the whole month?
The intention is obligatory for each day of Ramadan because each day is an independent act of worship separate from the others.
The intention must be made at night before the break of dawn, as the Prophetﷺ said: "Whoever does not intend fasting at night, there is no fast for him." [An-Nasa’i]
And he also said: "Whoever does not firmly resolve to fast before dawn, there is no fast for him." [At-Tirmidhi, Abu Dawood, and An-Nasa’i]
Whoever wakes up and eats Suhoor while mindful of fasting has made the intention. Likewise, one who firmly intends at any moment during the night to fast the next day has also fulfilled the intention.