the main reason for the decline in numbers on the BGY flights is quite simple.
the timings now mean you arrive at Bergamo at 2355, and so if you want to go on to Milan your not going to get there before 0100.
when the route was first reduced to Tue-Thu-Sat it used to arrive into BGY about 2000 which meant you could be sat in a restaurant in Bergamo by 2045