

This is the main reason of the question because the preposition in is used for time periods. But morning, afternoon and evening represent a period of time during the daytime where activities were going on. It represents the dark hours and the late time of the day. In olden times, when the time expression "at night" was originated, night might have been thought as a point of time in the day because there wasn't any activity going on and people were sleeping that time unlike daytime.

The origin of "at night" to indicate a point of time and the usage of prepositions "in" and"at" The bottom line is "it's idiomatic" as mentioned but I can offer the below rationale:ġ.
