They do land, so if you can find one of their hilltop nests you can shoot them when they come in. I've bagged a couple this way, but lost one when it fell down the cliff-side and disappeared into a crack between rocks.
Yup, just witnessed it first time ever today myself. A hawk landed in the nest in a tree. Shot it down with a Firebolt. IIRC, yesterday I was able to shoot a hawk down from the fly. You can do both still in 1.3.
I, too, suspect that the problems must be with respawned individuals. I haven't shot many of them off the sky (maybe around seven, and with at least two different characters), but whenever I've shot, it's worked.