This might be a rediculous question.

1 Does anyone have any though why 'at' is used with night? not in?

(in the morning, in the afternoo, in the evening but not in the night.)

2. One more question is why we usually put 'the' like in the morning, in the afternoon but not at the night)
Prepositions are somewhat... arbitrary. As Clive says sometimes, there's no good reason other than "We say them that way because we say them that way."
At noon.
The morning but not at the noon.
Students: We have free audio pronunciation exercises.
At noon, at night, at daybreak, at sunset ....
In the evening, in the afternoon, ....
Now can you figure out why ?
 BarbaraPA's reply was promoted to an answer.