Is prayer nullified by having thoughts while performing it?
Prayer isn`t nullified by having thoughts while performing it, provided that the praying person offers all of its pillars and meets all of its conditions. However, the reward decreases significantly in the absence of reverence since a praying person is rewarded according to the attentiveness of his/her heart during prayer.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
Should nail polish be removed before making ablution?
Yes, it should be removed because it prevents water from reaching the nails.
Is it permissible for someone who has forgotten to mention the supplication pertaining to answering the call of nature to say it while in the toilet?
It is disliked for a Muslim to mention Allah while in the toilet, but he/she may recall the supplication in his/her head without uttering it; that is in case he/she had forgotten mentioning it before entering the toilet.