Is it permissible to make up for the missed fasts of the deceased?

A deceased`s missed fasts should be made up for by his/her guardian. It is also permissible to make up for the missed fasts of a deceased relative, and to pay a ransom in expiation for the latter`s missed fasts, which is feeding a needy person for every missed day. However, the guardian`s permission need to be sought by the non-relatives of the dead to fast on his behalf. And Allah Knows Best.

 Is it permissible to pay the Zakah to my grandmother who lives alone in a rented accommodation with bad conditions noting she had three sons. 

Zakah cannot be given to ascendants (parents and grandparents). It is obligatory for her sons and grandsons to provide for her, and they would be sinful if they fail to do so. And Allah Knows Best.

What is the ruling on working for a company that manufactures cigarettes?

All Perfect Praise is due to Allah, The Lord of The Worlds

Working for a company that manufactures cigarettes is forbidden because smoking itself is forbidden, so its production, selling and circulation are forbidden as a result since they aid in committing sin, and whoever aids in that is like the sinner himself. And Allah Knows Best.

Is it permissible to make up for missed fast after the beginning of the second half of the month of Sha`ban (the month before Ramadan)?

Yes, it is permissible, but one who had missed fasts should hasten to make up for them. As for the Hadith mentioned in this regard, the prohibition is for offering absolute voluntary fasting. And Allah Knows Best.