Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
What is the ruling on one who sees moisture on his clothes and doubts whether it is semen or pre-seminal fluid (madhy)?
Whoever finds moisture upon waking from sleep and doubts whether it is semen or madhy, and cannot distinguish between them, he may choose between them and act according to his choice. If he wishes, he can consider it semen and perform the ritual bath, or consider it madhy, perform ablution, and wash what it has soiled. This is because if he fulfills the requirement of one of them, he is definitively free from it, and the default is his innocence from the other. And Allah the Almighty knows best.
What is the ruling on performing ablution (wudu') and ritual bathing (ghusl) with Zamzam water?
It is permissible to perform ablution and ritual bathing with Zamzam water. However, scholars disliked using it for cleaning after relieving oneself (istinja'). And Allah the Almighty knows best.
What do you say about someone who stays up all night on Laylat al-Qadr but misses Fajr prayer?
Such a person has deprived themselves of a great reward. Performing obligatory acts is more beloved to Allah than voluntary acts. Fajr prayer is an obligation, and performing it in congregation is equivalent to worshiping for the entire night. So how can someone neglect it while striving for voluntary prayers?!