Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
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 to combine and shorten prayers at home before traveling?
It is impermissible to combine and shorten prayers at home before traveling because a person is called a traveler once he/she departs the borders of his/her country, and offering prayer that way was originally intended to exempt a traveler. And Allah Knows Best.
Is it permissible for a girl to wear colored contact lenses?
All Perfect Praise is due to Allah, The Lord of The Worlds.
Wearing colored contact lenses for medical treatment is permissible, and wearing them as an adornment is also permissible, provided that she isn`t seen while having them on by non-Mahrams. And Alalh Knows Best.