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.

What should a person who was favored from Allah with a newborn, but couldn`t afford an Aqeeqah, do?

Aqeeqah (the sheep slaughtered on the seventh day from the child`s birth) is a desirable Sunnah for the financially able since Allah, The Exalted, charges not a soul beyond its capacity. Therefore, if the father couldn`t afford the Aqeeqah before the end of his wife`s confinement, then it isn`t due on him, and if he was able to afford it later on, then it is permissible, but if he didn`t until the child reached puberty, the latter can offer the Aqeeqah himself.

What is the ruling on performing voluntary prayers during official working hours?

All perfect praise be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions

There is no harm if  there was break time during official working hours, but if not then it is impermissible. And Allah Knows Best.

Is it permissible for a woman to shake hands with her brother-in-law?

It is forbidden for the woman to shake hands with her brother-in-law because he isn`t a Mahram (unmarriageable) of hers.