As has been said the portion of the crust below the lithosphere deforms plastically (i.e. over long periods of time it flows). So over time cracks will fill in. The deeper mantle is not very suitable for maintaining long term features like this.
We know the structure of the lithosphere and athenosphere from seismic surveys - if they were rigid enough to keep these cracks then they would have to be rigid enough to propagate wave differently.