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.
Someone wiped over his shoes after wearing them in a state of purity, then took them off and prayed without them?
Ablution is not invalidated by taking off leather socks or shoes after wiping over them. However, whoever takes them off after wiping must wash his feet only. If he prayed without washing his feet, he must wash his feet and repeat the prayer. And Allah the Almighty knows best.
What is the best manner in distributing the meat of the Aqeeqah?
It is better to divide all of it as cooked meat amongst the poor and the needy. Dividing it into three portions is a Sunnah, but it is permissible to keep all of it provided that a portion, even a small one, is given to the poor and needy (one kilo for example).
Is it permissible for a praying person to make supplication in each Sajdah (a prostration) of obligatory prayer?
It is permissible for a praying person, whether praying individually, or in congregation, to make supplication during Sujood (prostration) in obligatory, or voluntary prayers. However, it is disliked for the Imam to do so since he is required to spare the prayer performers any sort of hardship, unless he is leading a certain group who don`t mind him extending the prayer.