Should water be put in the deceased`s mouth and nose while washing him/her?

Putting water in the mouth and nose of the deceased while washing him is impermissible.

What is the ruling on smoking?

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

Smoking is forbidden (Haram) since it is harmful to one`s health as confirmed by trustful physicians, and Islam has forbidden taking anything that causes harm. The Prophet (PBUH) said: "There should be neither harm nor reciprocated harm." [Ibn Majah and Ahmad]. And Allah Knows Best.

Is it permissible for a pious Muslim woman to stay with her husband who had quit praying out of laziness?

Quitting prayer is one of the major grave sins that come after disbelieving in Allah, but the wife of such a person isn`t considered divorced, rather, she should exert all her efforts in order to bring him back to the way of Islam. However, if his sin is likely to lure her from the way of Islam, then she had better separate from him by lawful means such as Mokhal`aa (When a wife pays a compensation for her husband in return for divorcing her). Moreover, if she exercises patience, and remains steadfast on her faith, then there is no harm in doing that.

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.