Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is the prayer of someone who didn`t face Quibla (Ka`ba direction) valid?
All perfect praise be to Allah,The Lord of The Worlds. Facing the Quibla is a condition for the validity of prayer, and the prayer of the person who hadn`t faced the direction of the Quibla is invalid, and he is obliged to repeat it. And Allah 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.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.