I can't think of a sentence commonly heard in my dialect of English that includes the phrase "by night." All I can think of is "fly-by-night" which is an idiom for a business that cheats people in one area for a time, then moves somewhere else to avoid the law.
We like to drive at night.
I only see them at night.
In these cases, the word at means during the... I don't think that the word by can be substituted here.