Biter buildings are ignored while at correct speed, but biters are not. Acceleration drops instantly to zero and vehicle takes damage or is destroyed.
Game version - 0.18

Also sometimes unprovoked "no fuel" pictogram appears on/near the shadow while flying.

In the logic of units (biters and splitters) there is no concept of the height of the target above the surface. That is, all objects are on the same plane. Therefore, biters inflict damage and destroy "flying" objects.
If the units are not modified by any modification, then they only cause damage. Modification can easily add a change, so that the character or vehicle slows down (up to a complete stop).
Fuel from the "shadow" can be removed only by a script of any modification.