High speed cameras were used to determine the number of flaps per second and wind tunnels to establish lift.
The wingbeat rate of 1000 beats per minute in the documentary was a none too accurate average. Depending on species, Hummingbirds can beat their wings at between 12 - 80 times per second.
The largest, the Giant Hummingbird, has a wingbeat rate of around 12 - 15 beats per second.
The Rufus and Ruby Throat beat their wings around 50 times per second and a study revealed that 75% of the lift was from the down beat and 25% from the up beat.
The Amethyst Woodstar Hummingbird was once recorded beating its wings 80 times per second and it is believed that the Bee Hummingbird, the smallest of the species, may be capable of even greater numbers of beats per second.
This extraordinarily high beat rate would be reduced during flight and the term 'beat' is perhaps a little missleading when the bird is hovering, since the wings move in a more circular motion, giving the hummingbirds the ability to be the only bird which can fly backwards.
Just how long a hummingbird can keep up the higher rate of beats per second, I don't know, but to extrapolate the beats per second into beats per minute might be wrong, since it is unlikely that the bird would hover continuously for such a length of time. To do so would result in the Bee Hummingbird being extrapolated to something in the order of 5400 beats per minute. I think it clear that the bird could not sustain such an effort.
I think the documentary quoted the number of beats in terms of minutes for effect. As I have done above, to say '5400 per minute' has more impact than to say '90 beats per second', which the Bee Hummingbird is thought to be capable of.