I can’t come up with any ways to show the flight corridors without it being visible, but maybe you could instead have the hovercraft move very predictably when at low altitude to make them easy to avoid.
For example, when landing, they could move directly above the landing pad while at cruising altitude, then descend directly downwards which would be obvious and easy to avoid, and the birds would know to avoid the space directly above landing pads.
If the sudden changes in direction are a problem, maybe you could have sort of indicator lights to show when a hovercraft is about to change direction.