Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
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.
Is it permissible to make ablution without answering the call of nature after waking up?
Washing front and back openings (Istinjaa`) is not a condition for the validity of ablution because it is done to remove Najaasah (impurity), thus if there is no Najaasah, there is no need for that, and then it is permissible to make ablution without answering the call of nature. However, prayer is invalidated if there is Najaasah on the anus ,or the front opening, so it (Najaasah) must be removed for the prayer to become valid, and not the ablution.
Should one who doesn`t perform prayer out of laziness make it up later, and how should he/she do so?
All perfect praise be to Allah,The Lord of The Worlds He/she is obliged to make up missed prayers by offering with each obligatory prayer another one, and if he/she offers two, then it is better. And Allah Knows Best.