Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is the father a Mahram (Non-marriageable) to his son`s mother-in-law?
The father is a non-Mahram (Marriageable) to his son`s mother-in-law, so it is impermissible for them to look at each other, or to have a seclusion (Khalwah).
What is the ruling on performing the Istikhara prayer after the Witr paryer?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
The Istikhara prayer (Prayer for seeking guidance) is a Sunnah. It consists of two units (rak’ahs) performed outside of the obligatory prayers, after which the person supplicates with the traditionally narrated du’a. It is permissible to perform it before or after the Witr prayer, as the Istikhara prayer is recommended at all times except during the disliked times—the periods in which prayer is prohibited. This is because its specific reason (the Istikhara and supplication) occurs after the prayer itself, and any prayer with a subsequent reason is not permitted during the prohibited times. It should be noted that the two rak’ahs of Istikhara are not fulfilled by performing only one rak’ah, nor by a prostration of recitation (Sajdat al-Tilawah), nor by a funeral prayer (Janazah). And Allah the Exalted knows best.
Is it permissible to trim the eyebrows if they become excessively long?
Trimming eyebrows is permissible if they become excessively long, yet; it is reprehensible. And Allah Knows Best.