What should the one performing the slaughter say at the time of slaughtering the 'aqīqah?
All praise is due to Allah, and may peace and blessings be upon our Master, the Messenger of Allah.
It is Sunnah to say the following supplication at the time of slaughtering the 'aqīqah:
"Bismillāhi wallāhu Akbar, Allāhumma laka wa ilayka, hādhihi 'aqīqatu fulān."
("In the name of Allah, and Allah is the Greatest. O Allah, this is for You and unto You — this is the 'aqīqah of [the child's name].")
This is based on what al-Bayhaqī narrated in Al-Sunan al-Kubrā (Vol.9/P.511), that the Prophet ﷺ said: "Slaughter it in his name and say: In the name of Allah, and Allah is the Greatest. O Allah, this is for You and unto You — this is the 'aqīqah of so-and-so."
And Allah Almighty knows best.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Who should pay the Zakah (obligatory charity) from the orphan`s money?
His/her guardian, and if the latter fails to do so, then the orphan himself/herself is obliged to pay the Zakah once he/she reaches puberty, and is capable of handling his/her own affairs. And Allah Knows Best.
Is Zakah (obligatory charity) due on articles of merchandise even if they were stacked in the merchant`s stores for years?
Yes, Zakah is due on goods even if they were stacked in merchant`s stores for years, in this manner Islam struggle against monopoly.