Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it permissible to slaughter one animal as a sacrifice and an Aqeeqah (the sheep slaughtered on the seventh day from the child`s birth)?
It is impermissible to do so since each of them is slaughtered for a different reason.
In the last verse of Surah At-Tin, Allah Says (What means): "Is Allah not the most just of judges?" [At-Tin/8]. Is it permissible for us, while performing congregational prayer, to respond after the Imam recites it by saying: "Indeed, and I am among those who bear witness to that." ?
It is recommended for the worshipper to say 'Indeed' (Bala) silently after reciting or hearing the verse (/What means): "Is Allah not the most just of judges?" [At-Tin/8]. This is part of reflecting on the Quran during its recitation or listening, as Allah Says (What means): "Then do they not reflect upon the Quran, or are there locks upon [their] hearts?" (Muhammad: 24). Doing so helps in achieving humility and focus in prayer. And Allah Knows Best
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.