Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
Is Zakah (obligatory charity) due on the items used in the trading process such as: cars , shops etc..?
No Zakah is due on equipments used in the trading process such as cars and the like.
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.
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.