Lord Krishna was a Cowherd "Gaupal", he used to en·tice the animals and humans by his flute playing in vrudavana. This custom were followed since ancient times by most Cowherd, of playing flute to call their animals back and to show the way toward him. Since flute has long history with Cowherd and cows. By playing it at night would agitate the cows, and other animals. The second thought might be is, as the wind instrument "Basuri" or flute has "Karun" (करुण स्वर) or tender sound, which might evoke sadness in our minds at night time. So it might have been not advised to play flute at night.
The answer is more philosophical, but its based on our beliefs and stories told by our parents, thus may not have valid references but is centered towards the Hindu philosophy of harmony with nature.
Sources-
Hindu Primary Sources: A Sectarian Reader.
By Carl Olson page no - 297
World Flutelore: Folktales, Myths, and Other Stories of Magical Flute Power.
By Dale A. Olsen - page no. 196
These are avaliable on google books.