What is the ruling on one who performs ablution or the ritual bath while having nail polish?
Nail polish must be removed before ablution or ritual bath so that water reaches what is beneath it, because it is a barrier that prevents water from reaching that area. This is based on the hadith narrated by Ali (may Allah be pleased with him) from the Prophet (peace be upon him): "Whoever leaves a hair's breadth of his body unwashed from major impurity, such and such will be done to him in the Fire." (Reported by al-Bukhari). And Allah the Almighty knows best.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.