Footprints are connected to the model and so they will always be invisible, if the unit itself is invisible. You will have to use a workaround. Maybe if you have two models of the same unit. The first is the normal unit without footprints and the second one is the unit with only its footprints. The "footprint" unit would always be at the same position as the normal unit. Using the locust ability on the footprint model, other units won't be able to interact with it. Locust makes a unit invulnerable, untargetable, unselectable, does not show health bar and probably a lot more things.
If you think of the locusts from locust swarm, these are actual units, but have the locust ability, so you can't interact with them.
It's a lot work and I doubt it's worth it. Hopefully there is an easier solution, but I can't think of any right now.